Index

_

__init__() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.AnnotationTable method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.CustomAnnotation method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOCustomIntercell method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) (pypath.core.attrs.AttributeHandler method) (pypath.core.complex.AbstractComplexResource method) (pypath.core.complex.Cellchatdb method) (pypath.core.complex.Cellinker method) (pypath.core.complex.CellPhoneDB method) (pypath.core.complex.Compleat method) (pypath.core.complex.ComplexAggregator method) (pypath.core.complex.ComplexPortal method) (pypath.core.complex.Corum method) (pypath.core.complex.GuideToPharmacology method) (pypath.core.complex.Havugimana method) (pypath.core.complex.Hpmr method) (pypath.core.complex.Humap method) (pypath.core.complex.Humap2 method) (pypath.core.complex.Icellnet method) (pypath.core.complex.Kegg method) (pypath.core.complex.Pdb method) (pypath.core.complex.Signor method) (pypath.core.complex.Spike method) (pypath.core.entity.Entity method) (pypath.core.entity.EntityKey method) (pypath.core.entity.EntityList method) (pypath.core.enz_sub.EnzymeSubstrateAggregator method) (pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method) (pypath.core.enz_sub.EnzymeSubstrateProcessor method) (pypath.core.evidence.Evidence method) (pypath.core.evidence.Evidences method) (pypath.core.interaction.Interaction method) (pypath.core.interaction.InteractionDataFrameRecord method) (pypath.core.interaction.InteractionKey method) (pypath.core.intercell.IntercellAnnotation method) (pypath.core.network.Network method) (pypath.core.network.NetworkEntityCollection method) (pypath.core.network.NetworkStatsRecord method) (pypath.inputs.adrecs.AdrecsAdr method) (pypath.inputs.adrecs.AdrecsChildParent method) (pypath.inputs.adrecs.AdrecsDrug method) (pypath.inputs.adrecs.AdrecsDrugAdr method) (pypath.inputs.adrecs.AdrecsTerm method) (pypath.inputs.biogps.BiogpsDataset method) (pypath.inputs.cellinker.CellinkerInteraction method) (pypath.inputs.cellphonedb.CellPhoneDBAnnotation method) (pypath.inputs.dorothea.DorotheaInteraction method) (pypath.inputs.drugbank.DrugbankFull method) (pypath.inputs.gutmgene.GutmgeneAnnotation method) (pypath.inputs.gutmgene.GutmgeneRaw method) (pypath.inputs.hmdb.schema.common.Field method) (pypath.inputs.hpmr.HpmrInteraction method) (pypath.inputs.icellnet.IcellnetRecord method) (pypath.inputs.iptmnet.IptmnetInteraction method) (pypath.inputs.kegg.KeggPathway method) (pypath.inputs.lrdb.LrdbAnnotation method) (pypath.inputs.pathophenodb.DiseasePathogen method) (pypath.inputs.pathwaycommons.PathwayCommonsInteraction method) (pypath.inputs.pathwaycommons.PathwayCommonsResource method) (pypath.inputs.pisa.PisaBond method) (pypath.inputs.sider.SiderDrug method) (pypath.inputs.sider.SiderSideeffect method) (pypath.inputs.sider.SiderSideeffectMeddra method) (pypath.inputs.sider.SiderSideeffetFrequency method) (pypath.inputs.uniprot.Taxon method) (pypath.inputs.uniprot.UniprotQuery method) (pypath.inputs.uniprot.UniprotRecordHistory method) (pypath.internals.annot_formats.AnnotationGroup method) (pypath.internals.annot_formats.AnnotDef method) (pypath.internals.annot_formats.AnnotDefKey method) (pypath.internals.annot_formats.AnnotOp method) (pypath.internals.input_formats.ArrayMapping method) (pypath.internals.input_formats.BiomartMapping method) (pypath.internals.input_formats.FileMapping method) (pypath.internals.input_formats.HmdbMapping method) (pypath.internals.input_formats.MappingInput method) (pypath.internals.input_formats.NetworkInput method) (pypath.internals.input_formats.PickleMapping method) (pypath.internals.input_formats.ProMapping method) (pypath.internals.input_formats.RampMapping method) (pypath.internals.input_formats.ReadList method) (pypath.internals.input_formats.UnichemMapping method) (pypath.internals.input_formats.UniprotListMapping method) (pypath.internals.input_formats.UniprotMapping method) (pypath.internals.intera.Complex method) (pypath.internals.intera.Domain method) (pypath.internals.intera.DomainDomain method) (pypath.internals.intera.DomainMotif method) (pypath.internals.intera.Interface method) (pypath.internals.intera.Motif method) (pypath.internals.intera.Ptm method) (pypath.internals.intera.Regulation method) (pypath.internals.intera.Residue method) (pypath.internals.license.License method) (pypath.internals.license.LicenseAttrib method) (pypath.internals.license.LicenseFeature method) (pypath.internals.license.LicensePurpose method) (pypath.internals.license.LicenseSharing method) (pypath.internals.refs.Reference method) (pypath.internals.resource.AbstractResource method) (pypath.internals.resource.EnzymeSubstrateResource method) (pypath.internals.resource.EnzymeSubstrateResourceKey method) (pypath.internals.resource.NetworkDataset method) (pypath.internals.resource.NetworkResource method) (pypath.internals.resource.NetworkResourceKey method) (pypath.internals.resource.ResourceAttributes method) (pypath.omnipath.app.DatabaseManager method) (pypath.omnipath.databases.define.DatabaseClass method) (pypath.omnipath.databases.define.DatabaseDefinition method) (pypath.omnipath.databases.define.DatabaseDefinitionManager method) (pypath.omnipath.export.Export method) (pypath.omnipath.server.build.WebserviceTables method) (pypath.omnipath.server.legacy.PypathServer method) (pypath.omnipath.server.run.BaseServer method) (pypath.omnipath.server.run.Rest method) (pypath.omnipath.server.run.TableServer method) (pypath.omnipath.server.run.TwistedWebResource method) (pypath.omnipath.server.run.TwistedWebSite method) (pypath.resources.controller.ResourceController method) (pypath.resources.licenses.Licenses method) (pypath.share.curl.cache_delete_off method) (pypath.share.curl.cache_delete_on method) (pypath.share.curl.cache_off method) (pypath.share.curl.cache_on method) (pypath.share.curl.cache_print_off method) (pypath.share.curl.cache_print_on method) (pypath.share.curl.Curl method) (pypath.share.curl.debug_off method) (pypath.share.curl.debug_on method) (pypath.share.curl.dryrun_off method) (pypath.share.curl.dryrun_on method) (pypath.share.curl.FileOpener method) (pypath.share.curl.preserve_off method) (pypath.share.curl.preserve_on method) (pypath.share.curl.RemoteFile method) (pypath.share.progress.Progress method) (pypath.utils.go.GeneOntology method) (pypath.utils.go.GOAnnotation method) (pypath.utils.go.GOCustomAnnotation method) (pypath.utils.mapping.Mapper method) (pypath.utils.mapping.MappingTable method) (pypath.utils.mapping.MappingTableKey method) (pypath.utils.mapping.MapReader method) (pypath.utils.orthology.EnsemblOrtholog method) (pypath.utils.orthology.EnsemblOrthology method) (pypath.utils.orthology.HomologeneOrtholog method) (pypath.utils.orthology.HomologeneOrthology method) (pypath.utils.orthology.OmaOrtholog method) (pypath.utils.orthology.OmaOrthology method) (pypath.utils.orthology.OrthologBase method) (pypath.utils.orthology.OrthologMeta method) (pypath.utils.orthology.OrthologyManager method) (pypath.utils.orthology.OrthologyTableKey method) (pypath.utils.orthology.ProteinOrthology method) (pypath.utils.orthology.Proteomes method) (pypath.utils.orthology.PtmOrthology method) (pypath.utils.orthology.SequenceContainer method) (pypath.utils.pdb.Residue method) (pypath.utils.pdb.ResidueMapper method) (pypath.utils.pdb.Segment method) (pypath.utils.proteomicsdb.ProteomicsDB method) (pypath.utils.pyreact.AttributeHandler method) (pypath.utils.pyreact.BioPaxReader method) (pypath.utils.pyreact.Complex method) (pypath.utils.pyreact.ComplexVariations method) (pypath.utils.pyreact.Control method) (pypath.utils.pyreact.Entity method) (pypath.utils.pyreact.EntitySet method) (pypath.utils.pyreact.Intersecting method) (pypath.utils.pyreact.Protein method) (pypath.utils.pyreact.ProteinFamily method) (pypath.utils.pyreact.PyReact method) (pypath.utils.pyreact.Reaction method) (pypath.utils.pyreact.ReactionSide method) (pypath.utils.pyreact.Reference method) (pypath.utils.reflists.ReferenceListManager method) (pypath.utils.residues.ResidueMapper method) (pypath.utils.seq.Pfam method) (pypath.utils.seq.Resource method) (pypath.utils.seq.Seq method) (pypath.utils.unichem.Unichem method) (pypath.utils.uniprot.UniprotProtein method) (pypath.visual.drawing.InterSet method) (pypath.visual.drawing.Plot method) (pypath.visual.igraph_drawing.AbstractCairoGraphDrawer method) (pypath.visual.igraph_drawing.DefaultGraphDrawerFFsupport method) (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method) (pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method) (pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method) (pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method) (pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method) (pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method) (pypath.visual.igraph_drawing.vertex.AbstractCairoDrawer method) (pypath.visual.igraph_drawing.vertex.AbstractCairoVertexDrawer method) (pypath.visual.igraph_drawing.vertex.AbstractDrawer method) (pypath.visual.igraph_drawing.vertex.AbstractVertexDrawer method) (pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer method)

__iter__() (pypath.inputs.uniprot.UniprotQuery method)

A

abs_interactions() (in module pypath.inputs.abs) AbstractCairoDrawer (class in pypath.visual.igraph_drawing.vertex) AbstractCairoGraphDrawer (class in pypath.visual.igraph_drawing) AbstractCairoVertexDrawer (class in pypath.visual.igraph_drawing.vertex) AbstractComplexResource (class in pypath.core.complex) AbstractDrawer (class in pypath.visual.igraph_drawing.vertex) AbstractEdgeDrawer (class in pypath.visual.igraph_drawing.edge) AbstractResource (class in pypath.internals.resource) AbstractVertexDrawer (class in pypath.visual.igraph_drawing.vertex) ac() (in module pypath.utils.uniprot) acsn_biopax() (in module pypath.inputs.reaction) acsn_interactions() (in module pypath.inputs.acsn) acsn_interactions_2() (in module pypath.inputs.reaction) acsn_interactions_sif() (in module pypath.inputs.acsn) activated_by (pypath.core.network.Network attribute) activates (pypath.core.network.Network attribute) activity_flow (in module pypath.resources.data_formats) activity_regulation() (in module pypath.utils.uniprot) activity_regulation_with_xrefs() (in module pypath.utils.uniprot) add_attr() (pypath.internals.intera.Complex method) add_complexes_by_inference() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) add_evidence() (pypath.core.interaction.Interaction method) add_extra_fields() (pypath.omnipath.export.Export method) add_interaction() (pypath.core.network.Network method) add_node() (pypath.core.network.Network method) add_residues() (pypath.internals.intera.Interface method) add_resource_attrs() (pypath.resources.controller.ResourceController method) add_sign() (pypath.core.interaction.Interaction method) Adhesome (class in pypath.core.annot) adhesome_annotations() (in module pypath.inputs.adhesome) adhesome_interactions() (in module pypath.inputs.adhesome) adr (pypath.inputs.adrecs.AdrecsDrugAdr attribute) adr_badd (pypath.inputs.adrecs.AdrecsDrugAdr attribute) adr_class (pypath.inputs.adrecs.AdrecsAdr attribute) adrecs_adr_ontology() (in module pypath.inputs.adrecs) adrecs_class (pypath.inputs.adrecs.AdrecsTerm attribute) adrecs_drug_adr() (in module pypath.inputs.adrecs) adrecs_drug_identifiers() (in module pypath.inputs.adrecs) adrecs_hierarchy() (in module pypath.inputs.adrecs) AdrecsAdr (class in pypath.inputs.adrecs) AdrecsChildParent (class in pypath.inputs.adrecs) AdrecsDrug (class in pypath.inputs.adrecs) AdrecsDrugAdr (class in pypath.inputs.adrecs) AdrecsTerm (class in pypath.inputs.adrecs) all_annotations() (pypath.core.annot.AnnotationTable method) all_annotations_str() (pypath.core.annot.AnnotationTable method) all_complexes() (in module pypath.core.complex) (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) all_entities() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) all_from_aspect() (pypath.utils.go.GeneOntology method) all_mirnas() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method)

all_proteins() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) all_refs() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) all_sources (pypath.inputs.dorothea.DorotheaInteraction attribute) all_swissprots() (in module pypath.inputs.uniprot_db) all_trembls() (in module pypath.inputs.uniprot_db) all_uniprots() (in module pypath.inputs.uniprot_db) (pypath.utils.go.GOAnnotation method) Almen2009 (class in pypath.core.annot) almen2009_annotations() (in module pypath.inputs.almen2009) AlphaVaryingEdgeDrawer (class in pypath.visual.igraph_drawing.edge) alternative_products() (in module pypath.utils.uniprot) alternative_products_with_xrefs() (in module pypath.utils.uniprot) annotate() (in module pypath.utils.go) annotate_complex() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) AnnotationBase (class in pypath.core.annot) AnnotationGroup (class in pypath.internals.annot_formats) AnnotationTable (class in pypath.core.annot) AnnotDef (class in pypath.internals.annot_formats) AnnotDefKey (class in pypath.internals.annot_formats) AnnotOp (class in pypath.internals.annot_formats) annots (pypath.internals.annot_formats.AnnotOp attribute) args (pypath.internals.annot_formats.AnnotDef attribute) arn_interactions() (in module pypath.inputs.netbiol) ArrayMapping (class in pypath.internals.input_formats) ArrowEdgeDrawer (class in pypath.visual.igraph_drawing.edge) (in module pypath.visual.igraph_drawing) asdict() (pypath.core.evidence.Evidence method) (pypath.core.evidence.Evidences method) (pypath.core.interaction.Interaction method) (pypath.utils.orthology.EnsemblOrthology method) (pypath.utils.orthology.HomologeneOrthology method) (pypath.utils.orthology.OmaOrthology method) (pypath.utils.orthology.ProteinOrthology method) aspect (pypath.internals.annot_formats.AnnotDef attribute) aspect_from_name() (pypath.utils.go.GeneOntology method) assign_to_network() (pypath.core.enz_sub.EnzymeSubstrateAggregator method) atc (pypath.inputs.sider.SiderDrug attribute) AttributeHandler (class in pypath.core.attrs) (class in pypath.utils.pyreact) attrs (pypath.core.evidence.Evidences property) avoid (pypath.internals.annot_formats.AnnotDef attribute)

B

Baccin2019 (class in pypath.core.annot) baccin2019_annotations() (in module pypath.inputs.baccin2019) baccin2019_interactions() (in module pypath.inputs.baccin2019) badd (pypath.inputs.adrecs.AdrecsAdr attribute) (pypath.inputs.adrecs.AdrecsDrug attribute) (pypath.inputs.adrecs.AdrecsTerm attribute) BaseServer (class in pypath.omnipath.server.run) Biogps (class in pypath.core.annot) biogps_annotations() (in module pypath.inputs.biogps) biogps_datasets() (in module pypath.inputs.biogps) biogps_download() (in module pypath.inputs.biogps) biogps_download_all() (in module pypath.inputs.biogps) BiogpsDataset (class in pypath.inputs.biogps) biogrid_all_interactions() (in module pypath.inputs.biogrid) biogrid_interactions() (in module pypath.inputs.biogrid) biomart_homology() (in module pypath.inputs.biomart) biomart_microarray() (in module pypath.inputs.biomart) biomart_microarray_types() (in module pypath.inputs.biomart) biomart_microarrays() (in module pypath.inputs.biomart) biomart_query() (in module pypath.inputs.biomart) BiomartMapping (class in pypath.internals.input_formats) biopax_size() (pypath.utils.pyreact.BioPaxReader method) BioPaxReader (class in pypath.utils.pyreact) bond_types() (pypath.internals.intera.Interface method) browse() (in module pypath.utils.uniprot) (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.CustomAnnotation method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) (pypath.core.intercell.IntercellAnnotation method)

build() (in module pypath.omnipath.databases) (pypath.omnipath.app.DatabaseManager method) (pypath.omnipath.databases.define.DatabaseDefinitionManager method) build_dataset() (pypath.omnipath.app.DatabaseManager method) build_list() (pypath.core.enz_sub.EnzymeSubstrateAggregator method) by_category (pypath.core.network.NetworkStatsRecord attribute) by_resource (pypath.core.network.NetworkStatsRecord attribute)

C

ca1_interactions() (in module pypath.inputs.ca1) cache_delete_off (class in pypath.share.curl) cache_delete_on (class in pypath.share.curl) cache_item() (in module pypath.share.cache) cache_off (class in pypath.share.curl) cache_on (class in pypath.share.curl) cache_path() (in module pypath.share.cache) (pypath.share.curl.Curl class method) cache_print_off (class in pypath.share.curl) cache_print_on (class in pypath.share.curl) cancer_gene_census_annotations() (in module pypath.inputs.cosmic) Cancerdrugsdb (class in pypath.core.annot) cancerdrugsdb_annotations() (in module pypath.inputs.cancerdrugsdb) cancerdrugsdb_download() (in module pypath.inputs.cancerdrugsdb) cancerdrugsdb_interactions() (in module pypath.inputs.cancerdrugsdb) CancerGeneCensus (class in pypath.core.annot) Cancersea (class in pypath.core.annot) cancersea_annotations() (in module pypath.inputs.cancersea) cat_resource (pypath.core.network.NetworkStatsRecord attribute) catalytic_activity() (in module pypath.utils.uniprot) catalytic_activity_with_xrefs() (in module pypath.utils.uniprot) ccmap_interactions() (in module pypath.inputs.cancercellmap) cell_supplementary() (in module pypath.inputs.cell) cell_type (pypath.inputs.lrdb.LrdbAnnotation attribute) Cellcall (class in pypath.core.annot) cellcall_annotations() (in module pypath.inputs.cellcall) cellcall_download() (in module pypath.inputs.cellcall) cellcall_download_all() (in module pypath.inputs.cellcall) cellcall_interactions() (in module pypath.inputs.cellcall) Cellcellinteractions (class in pypath.core.annot) cellcellinteractions_annotations() (in module pypath.inputs.cellcellinteractions) Cellchatdb (class in pypath.core.annot) (class in pypath.core.complex) cellchatdb_annotations() (in module pypath.inputs.cellchatdb) cellchatdb_cofactors() (in module pypath.inputs.cellchatdb) cellchatdb_complexes() (in module pypath.inputs.cellchatdb) cellchatdb_download() (in module pypath.inputs.cellchatdb) cellchatdb_interactions() (in module pypath.inputs.cellchatdb) CellchatdbComplex (class in pypath.core.annot) Cellinker (class in pypath.core.annot) (class in pypath.core.complex) cellinker_annotations() (in module pypath.inputs.cellinker) cellinker_complex_annotations() (in module pypath.inputs.cellinker) cellinker_complexes() (in module pypath.inputs.cellinker) cellinker_complexes_raw() (in module pypath.inputs.cellinker) cellinker_lr_interactions() (in module pypath.inputs.cellinker) cellinker_lr_interactions_raw() (in module pypath.inputs.cellinker) cellinker_protein_annotations() (in module pypath.inputs.cellinker) cellinker_smol_interactions() (in module pypath.inputs.cellinker) cellinker_smol_interactions_raw() (in module pypath.inputs.cellinker) CellinkerComplex (class in pypath.core.annot) CellinkerInteraction (class in pypath.inputs.cellinker) CellPhoneDB (class in pypath.core.annot) (class in pypath.core.complex) cellphonedb_complex_annotations() (in module pypath.inputs.cellphonedb) cellphonedb_complexes() (in module pypath.inputs.cellphonedb) cellphonedb_interactions() (in module pypath.inputs.cellphonedb) cellphonedb_ligands_receptors() (in module pypath.inputs.cellphonedb) cellphonedb_protein_annotations() (in module pypath.inputs.cellphonedb) CellPhoneDBAnnotation (class in pypath.inputs.cellphonedb) CellPhoneDBComplex (class in pypath.core.annot) CellSurfaceProteinAtlas (class in pypath.core.annot) CellSurfaceProteinAtlasCellType (class in pypath.core.annot) Celltalkdb (class in pypath.core.annot) celltalkdb_annotations() (in module pypath.inputs.celltalkdb) celltalkdb_download() (in module pypath.inputs.celltalkdb) celltalkdb_interactions() (in module pypath.inputs.celltalkdb) Celltypist (class in pypath.core.annot) celltypist_annotations() (in module pypath.inputs.celltypist) chain (pypath.utils.pdb.Residue attribute) chain_1 (pypath.inputs.pisa.PisaBond attribute) chain_2 (pypath.inputs.pisa.PisaBond attribute) chain_map() (pypath.utils.mapping.Mapper method) check() (in module pypath.utils.reflists) (pypath.utils.reflists.ReferenceListManager method) check_level() (pypath.internals.license.LicenseAttrib class method) (pypath.internals.license.LicenseFeature class method) (pypath.internals.license.LicensePurpose class method) (pypath.internals.license.LicenseSharing class method) chembl_activities() (in module pypath.inputs.chembl) chembl_assays() (in module pypath.inputs.chembl) chembl_documents() (in module pypath.inputs.chembl) chembl_drug_indications() (in module pypath.inputs.chembl) chembl_mechanisms() (in module pypath.inputs.chembl) chembl_molecules() (in module pypath.inputs.chembl) chembl_targets() (in module pypath.inputs.chembl) child (pypath.inputs.adrecs.AdrecsChildParent attribute) chipseq (pypath.inputs.dorothea.DorotheaInteraction attribute) chipseq_sources (pypath.inputs.dorothea.DorotheaInteraction attribute) cid (pypath.inputs.sider.SiderSideeffectMeddra attribute) class_and_param() (in module pypath.omnipath.databases) (pypath.omnipath.databases.define.DatabaseDefinitionManager method) class_to_class_connections() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) classes_by_entity() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) classification (pypath.inputs.gutmgene.GutmgeneAnnotation attribute) (pypath.inputs.gutmgene.GutmgeneRaw attribute) (pypath.inputs.icellnet.IcellnetRecord attribute) clean() (pypath.utils.pdb.ResidueMapper method) (pypath.utils.residues.ResidueMapper method) cleanup_hook() (pypath.utils.pyreact.BioPaxReader method) clear() (pypath.internals.resource.NetworkDataset method) clinvar_citations() (in module pypath.inputs.clinvar) clinvar_raw() (in module pypath.inputs.clinvar) close() (pypath.share.curl.Curl method) close_biopax() (pypath.utils.pyreact.BioPaxReader method) coexp (pypath.inputs.dorothea.DorotheaInteraction attribute) coexp_sources (pypath.inputs.dorothea.DorotheaInteraction attribute) collect() (in module pypath.utils.uniprot) collect_complex_identifiers (pypath.core.network.Network attribute) collect_complex_labels (pypath.core.network.Network attribute) collect_complexes (pypath.core.network.Network attribute) collect_curation_effort (pypath.core.network.Network attribute) collect_data_models (pypath.core.network.Network attribute) collect_datasets (pypath.core.network.Network attribute) collect_degrees_directed (pypath.core.network.Network attribute) collect_degrees_directed_in (pypath.core.network.Network attribute) collect_degrees_directed_out (pypath.core.network.Network attribute) collect_degrees_negative (pypath.core.network.Network attribute) collect_degrees_negative_in (pypath.core.network.Network attribute) collect_degrees_negative_out (pypath.core.network.Network attribute) collect_degrees_non_directed (pypath.core.network.Network attribute) collect_degrees_positive (pypath.core.network.Network attribute) collect_degrees_positive_in (pypath.core.network.Network attribute) collect_degrees_positive_out (pypath.core.network.Network attribute) collect_degrees_signed (pypath.core.network.Network attribute) collect_degrees_signed_in (pypath.core.network.Network attribute) collect_degrees_signed_out (pypath.core.network.Network attribute) collect_degrees_undirected (pypath.core.network.Network attribute) collect_entities (pypath.core.network.Network attribute) collect_evidences (pypath.core.network.Network attribute) collect_identifiers (pypath.core.network.Network attribute) collect_interaction() (pypath.resources.controller.ResourceController method) collect_interaction_types (pypath.core.network.Network attribute) collect_interactions (pypath.core.network.Network attribute) collect_interactions_0 (pypath.core.network.Network attribute) collect_interactions_directed (pypath.core.network.Network attribute) collect_interactions_mutual (pypath.core.network.Network attribute) collect_interactions_negative (pypath.core.network.Network attribute) collect_interactions_non_directed (pypath.core.network.Network attribute) collect_interactions_non_directed_0 (pypath.core.network.Network attribute) collect_interactions_positive (pypath.core.network.Network attribute) collect_interactions_signed (pypath.core.network.Network attribute) collect_interactions_undirected (pypath.core.network.Network attribute) collect_interactions_undirected_0 (pypath.core.network.Network attribute) collect_labels (pypath.core.network.Network attribute) collect_lncrna_identifiers (pypath.core.network.Network attribute) collect_lncrna_labels (pypath.core.network.Network attribute) collect_lncrnas (pypath.core.network.Network attribute) collect_mirna_identifiers (pypath.core.network.Network attribute) collect_mirna_labels (pypath.core.network.Network attribute) collect_mirnas (pypath.core.network.Network attribute) collect_network() (pypath.resources.controller.ResourceController method) collect_protein_identifiers (pypath.core.network.Network attribute) collect_protein_labels (pypath.core.network.Network attribute) collect_proteins (pypath.core.network.Network attribute) collect_references (pypath.core.network.Network attribute) collect_resource_names (pypath.core.network.Network attribute) collect_resource_names_via (pypath.core.network.Network attribute) collect_resources (pypath.core.network.Network attribute) collect_resources_via (pypath.core.network.Network attribute) collect_small_molecule_identifiers (pypath.core.network.Network attribute) collect_small_molecule_labels (pypath.core.network.Network attribute) collect_small_molecules (pypath.core.network.Network attribute) collectri() (pypath.core.network.Network class method) collectri_interactions() (in module pypath.inputs.collectri) collectri_raw() (in module pypath.inputs.collectri) compath_mappings() (in module pypath.inputs.compath) compile_table() (pypath.omnipath.app.DatabaseManager method) compile_tables() (pypath.omnipath.app.DatabaseManager method) Compleat (class in pypath.core.complex) compleat_complexes() (in module pypath.inputs.compleat) compleat_raw() (in module pypath.inputs.compleat) Complex (class in pypath.internals.intera) (class in pypath.utils.pyreact) complex_identifiers_by_data_model (pypath.core.network.Network attribute) complex_identifiers_by_data_model() (pypath.core.interaction.Interaction method) complex_identifiers_by_interaction_type (pypath.core.network.Network attribute) complex_identifiers_by_interaction_type() (pypath.core.interaction.Interaction method) complex_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) complex_identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) complex_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) complex_identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) complex_identifiers_by_reference (pypath.core.network.Network attribute) complex_identifiers_by_reference() (pypath.core.interaction.Interaction method) complex_identifiers_by_resource (pypath.core.network.Network attribute) complex_identifiers_by_resource() (pypath.core.interaction.Interaction method) complex_inference() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) complex_labels_by_data_model (pypath.core.network.Network attribute) complex_labels_by_data_model() (pypath.core.interaction.Interaction method) complex_labels_by_interaction_type (pypath.core.network.Network attribute) complex_labels_by_interaction_type() (pypath.core.interaction.Interaction method) complex_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) complex_labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) complex_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) complex_labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) complex_labels_by_reference (pypath.core.network.Network attribute) complex_labels_by_reference() (pypath.core.interaction.Interaction method) complex_labels_by_resource (pypath.core.network.Network attribute) complex_labels_by_resource() (pypath.core.interaction.Interaction method) ComplexAggregator (class in pypath.core.complex) complexes_by_data_model (pypath.core.network.Network attribute) complexes_by_data_model() (pypath.core.interaction.Interaction method) complexes_by_interaction_type (pypath.core.network.Network attribute) complexes_by_interaction_type() (pypath.core.interaction.Interaction method) complexes_by_interaction_type_and_data_model (pypath.core.network.Network attribute) complexes_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) complexes_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) complexes_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) complexes_by_reference (pypath.core.network.Network attribute) complexes_by_reference() (pypath.core.interaction.Interaction method) complexes_by_resource (pypath.core.network.Network attribute) complexes_by_resource() (pypath.core.interaction.Interaction method) ComplexPortal (class in pypath.core.complex) complexportal_complexes() (in module pypath.inputs.complexportal) ComplexVariations (class in pypath.utils.pyreact) components_to_complex() (in module pypath.inputs.cellinker) Comppi (class in pypath.core.annot) comppi_interaction_locations() (in module pypath.inputs.comppi) comppi_locations() (in module pypath.inputs.comppi) connectivity_search() (pypath.utils.unichem.Unichem method) Connectomedb (class in pypath.core.annot) connectomedb_annotations() (in module pypath.inputs.connectomedb) connectomedb_interactions() (in module pypath.inputs.connectomedb) consensus() (pypath.core.interaction.Interaction method) consensus_edges() (pypath.core.interaction.Interaction method) construct_binary_data() (pypath.share.curl.Curl method) Control (class in pypath.utils.pyreact) Corum (class in pypath.core.annot) (class in pypath.core.complex) corum_complexes() (in module pypath.inputs.corum) CorumFuncat (class in pypath.core.annot) CorumGO (class in pypath.core.annot) count() (pypath.core.entity.EntityKey method) (pypath.core.interaction.InteractionDataFrameRecord method) (pypath.core.interaction.InteractionKey method) (pypath.core.network.NetworkStatsRecord method) (pypath.inputs.adrecs.AdrecsAdr method) (pypath.inputs.adrecs.AdrecsChildParent method) (pypath.inputs.adrecs.AdrecsDrug method) (pypath.inputs.adrecs.AdrecsDrugAdr method) (pypath.inputs.adrecs.AdrecsTerm method) (pypath.inputs.biogps.BiogpsDataset method) (pypath.inputs.cellinker.CellinkerInteraction method) (pypath.inputs.cellphonedb.CellPhoneDBAnnotation method) (pypath.inputs.dorothea.DorotheaInteraction method) (pypath.inputs.gutmgene.GutmgeneAnnotation method) (pypath.inputs.gutmgene.GutmgeneRaw method) (pypath.inputs.hpmr.HpmrInteraction method) (pypath.inputs.icellnet.IcellnetRecord method) (pypath.inputs.iptmnet.IptmnetInteraction method) (pypath.inputs.kegg.KeggPathway method) (pypath.inputs.lrdb.LrdbAnnotation method) (pypath.inputs.pathophenodb.DiseasePathogen method) (pypath.inputs.pathwaycommons.PathwayCommonsInteraction method) (pypath.inputs.pathwaycommons.PathwayCommonsResource method) (pypath.inputs.pisa.PisaBond method) (pypath.inputs.sider.SiderDrug method) (pypath.inputs.sider.SiderSideeffect method) (pypath.inputs.sider.SiderSideeffectMeddra method) (pypath.inputs.sider.SiderSideeffetFrequency method) (pypath.inputs.uniprot.Taxon method) (pypath.inputs.uniprot.UniprotRecordHistory method) (pypath.internals.annot_formats.AnnotDef method) (pypath.internals.annot_formats.AnnotDefKey method) (pypath.internals.annot_formats.AnnotOp method) (pypath.internals.resource.EnzymeSubstrateResourceKey method) (pypath.internals.resource.NetworkResourceKey method) (pypath.utils.mapping.MappingTableKey method) (pypath.utils.orthology.EnsemblOrtholog method) (pypath.utils.orthology.HomologeneOrtholog method) (pypath.utils.orthology.OmaOrtholog method) (pypath.utils.orthology.OrthologyTableKey method) (pypath.utils.pdb.Residue method) (pypath.utils.pdb.Segment method) count_activated_by (pypath.core.network.Network attribute) count_activates (pypath.core.network.Network attribute) count_complex_identifiers (pypath.core.network.Network attribute) count_complex_identifiers() (pypath.core.interaction.Interaction method) count_complex_identifiers_by_data_model (pypath.core.network.Network attribute) count_complex_identifiers_by_interaction_type (pypath.core.network.Network attribute) count_complex_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_complex_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_complex_identifiers_by_reference (pypath.core.network.Network attribute) count_complex_identifiers_by_resource (pypath.core.network.Network attribute) count_complex_labels (pypath.core.network.Network attribute) count_complex_labels() (pypath.core.interaction.Interaction method) count_complex_labels_by_data_model (pypath.core.network.Network attribute) count_complex_labels_by_interaction_type (pypath.core.network.Network attribute) count_complex_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_complex_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_complex_labels_by_reference (pypath.core.network.Network attribute) count_complex_labels_by_resource (pypath.core.network.Network attribute) count_complexes (pypath.core.network.Network attribute) count_complexes() (pypath.core.interaction.Interaction method) count_complexes_by_data_model (pypath.core.network.Network attribute) count_complexes_by_interaction_type (pypath.core.network.Network attribute) count_complexes_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_complexes_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_complexes_by_reference (pypath.core.network.Network attribute) count_complexes_by_resource (pypath.core.network.Network attribute) count_curation_effort (pypath.core.network.Network attribute) count_curation_effort_by_data_model (pypath.core.network.Network attribute) count_curation_effort_by_interaction_type (pypath.core.network.Network attribute) count_curation_effort_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_curation_effort_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_curation_effort_by_reference (pypath.core.network.Network attribute) count_curation_effort_by_resource (pypath.core.network.Network attribute) count_data_models (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_data_models_by_data_model (pypath.core.network.Network attribute) count_data_models_by_interaction_type (pypath.core.network.Network attribute) count_data_models_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_data_models_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_data_models_by_reference (pypath.core.network.Network attribute) count_data_models_by_resource (pypath.core.network.Network attribute) count_datasets (pypath.core.network.Network attribute) count_datasets_by_data_model (pypath.core.network.Network attribute) count_datasets_by_interaction_type (pypath.core.network.Network attribute) count_datasets_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_datasets_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_datasets_by_reference (pypath.core.network.Network attribute) count_datasets_by_resource (pypath.core.network.Network attribute) count_degrees_directed (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_directed_by_data_model (pypath.core.network.Network attribute) count_degrees_directed_by_interaction_type (pypath.core.network.Network attribute) count_degrees_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_directed_by_reference (pypath.core.network.Network attribute) count_degrees_directed_by_resource (pypath.core.network.Network attribute) count_degrees_directed_in (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_directed_in_by_data_model (pypath.core.network.Network attribute) count_degrees_directed_in_by_interaction_type (pypath.core.network.Network attribute) count_degrees_directed_in_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_directed_in_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_directed_in_by_reference (pypath.core.network.Network attribute) count_degrees_directed_in_by_resource (pypath.core.network.Network attribute) count_degrees_directed_out (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_directed_out_by_data_model (pypath.core.network.Network attribute) count_degrees_directed_out_by_interaction_type (pypath.core.network.Network attribute) count_degrees_directed_out_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_directed_out_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_directed_out_by_reference (pypath.core.network.Network attribute) count_degrees_directed_out_by_resource (pypath.core.network.Network attribute) count_degrees_negative (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_negative_by_data_model (pypath.core.network.Network attribute) count_degrees_negative_by_interaction_type (pypath.core.network.Network attribute) count_degrees_negative_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_negative_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_negative_by_reference (pypath.core.network.Network attribute) count_degrees_negative_by_resource (pypath.core.network.Network attribute) count_degrees_negative_in (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_negative_in_by_data_model (pypath.core.network.Network attribute) count_degrees_negative_in_by_interaction_type (pypath.core.network.Network attribute) count_degrees_negative_in_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_negative_in_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_negative_in_by_reference (pypath.core.network.Network attribute) count_degrees_negative_in_by_resource (pypath.core.network.Network attribute) count_degrees_negative_out (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_negative_out_by_data_model (pypath.core.network.Network attribute) count_degrees_negative_out_by_interaction_type (pypath.core.network.Network attribute) count_degrees_negative_out_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_negative_out_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_negative_out_by_reference (pypath.core.network.Network attribute) count_degrees_negative_out_by_resource (pypath.core.network.Network attribute) count_degrees_non_directed (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_non_directed_by_data_model (pypath.core.network.Network attribute) count_degrees_non_directed_by_interaction_type (pypath.core.network.Network attribute) count_degrees_non_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_non_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_non_directed_by_reference (pypath.core.network.Network attribute) count_degrees_non_directed_by_resource (pypath.core.network.Network attribute) count_degrees_positive (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_positive_by_data_model (pypath.core.network.Network attribute) count_degrees_positive_by_interaction_type (pypath.core.network.Network attribute) count_degrees_positive_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_positive_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_positive_by_reference (pypath.core.network.Network attribute) count_degrees_positive_by_resource (pypath.core.network.Network attribute) count_degrees_positive_in (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_positive_in_by_data_model (pypath.core.network.Network attribute) count_degrees_positive_in_by_interaction_type (pypath.core.network.Network attribute) count_degrees_positive_in_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_positive_in_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_positive_in_by_reference (pypath.core.network.Network attribute) count_degrees_positive_in_by_resource (pypath.core.network.Network attribute) count_degrees_positive_out (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_positive_out_by_data_model (pypath.core.network.Network attribute) count_degrees_positive_out_by_interaction_type (pypath.core.network.Network attribute) count_degrees_positive_out_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_positive_out_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_positive_out_by_reference (pypath.core.network.Network attribute) count_degrees_positive_out_by_resource (pypath.core.network.Network attribute) count_degrees_signed (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_signed_by_data_model (pypath.core.network.Network attribute) count_degrees_signed_by_interaction_type (pypath.core.network.Network attribute) count_degrees_signed_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_signed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_signed_by_reference (pypath.core.network.Network attribute) count_degrees_signed_by_resource (pypath.core.network.Network attribute) count_degrees_signed_in (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_signed_in_by_data_model (pypath.core.network.Network attribute) count_degrees_signed_in_by_interaction_type (pypath.core.network.Network attribute) count_degrees_signed_in_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_signed_in_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_signed_in_by_reference (pypath.core.network.Network attribute) count_degrees_signed_in_by_resource (pypath.core.network.Network attribute) count_degrees_signed_out (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute)

count_degrees_signed_out_by_data_model (pypath.core.network.Network attribute) count_degrees_signed_out_by_interaction_type (pypath.core.network.Network attribute) count_degrees_signed_out_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_signed_out_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_signed_out_by_reference (pypath.core.network.Network attribute) count_degrees_signed_out_by_resource (pypath.core.network.Network attribute) count_degrees_undirected (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_degrees_undirected_by_data_model (pypath.core.network.Network attribute) count_degrees_undirected_by_interaction_type (pypath.core.network.Network attribute) count_degrees_undirected_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_degrees_undirected_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_degrees_undirected_by_reference (pypath.core.network.Network attribute) count_degrees_undirected_by_resource (pypath.core.network.Network attribute) count_entities (pypath.core.network.Network attribute) count_entities() (pypath.core.interaction.Interaction method) count_entities_by_data_model (pypath.core.network.Network attribute) count_entities_by_interaction_type (pypath.core.network.Network attribute) count_entities_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_entities_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_entities_by_reference (pypath.core.network.Network attribute) count_entities_by_resource (pypath.core.network.Network attribute) count_entity_type() (pypath.core.entity.Entity class method) count_evidences (pypath.core.network.Network attribute) count_evidences_by_data_model (pypath.core.network.Network attribute) count_evidences_by_interaction_type (pypath.core.network.Network attribute) count_evidences_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_evidences_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_evidences_by_reference (pypath.core.network.Network attribute) count_evidences_by_resource (pypath.core.network.Network attribute) count_identifiers (pypath.core.network.Network attribute) count_identifiers() (pypath.core.interaction.Interaction method) count_identifiers_by_data_model (pypath.core.network.Network attribute) count_identifiers_by_interaction_type (pypath.core.network.Network attribute) count_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_identifiers_by_reference (pypath.core.network.Network attribute) count_identifiers_by_resource (pypath.core.network.Network attribute) count_interaction_types (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_interaction_types_by_data_model (pypath.core.network.Network attribute) count_interaction_types_by_interaction_type (pypath.core.network.Network attribute) count_interaction_types_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interaction_types_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interaction_types_by_reference (pypath.core.network.Network attribute) count_interaction_types_by_resource (pypath.core.network.Network attribute) count_interactions (pypath.core.network.Network attribute) count_interactions() (pypath.core.interaction.Interaction method) count_interactions_0 (pypath.core.network.Network attribute) count_interactions_0() (pypath.core.interaction.Interaction method) count_interactions_0_by_data_model (pypath.core.network.Network attribute) count_interactions_0_by_interaction_type (pypath.core.network.Network attribute) count_interactions_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interactions_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interactions_0_by_reference (pypath.core.network.Network attribute) count_interactions_0_by_resource (pypath.core.network.Network attribute) count_interactions_by_data_model (pypath.core.network.Network attribute) count_interactions_by_interaction_type (pypath.core.network.Network attribute) count_interactions_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interactions_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interactions_by_reference (pypath.core.network.Network attribute) count_interactions_by_resource (pypath.core.network.Network attribute) count_interactions_directed (pypath.core.network.Network attribute) count_interactions_directed() (pypath.core.interaction.Interaction method) count_interactions_directed_by_data_model (pypath.core.network.Network attribute) count_interactions_directed_by_interaction_type (pypath.core.network.Network attribute) count_interactions_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interactions_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interactions_directed_by_reference (pypath.core.network.Network attribute) count_interactions_directed_by_resource (pypath.core.network.Network attribute) count_interactions_mutual (pypath.core.network.Network attribute) count_interactions_mutual() (pypath.core.interaction.Interaction method) count_interactions_mutual_by_data_model (pypath.core.network.Network attribute) count_interactions_mutual_by_interaction_type (pypath.core.network.Network attribute) count_interactions_mutual_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interactions_mutual_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interactions_mutual_by_reference (pypath.core.network.Network attribute) count_interactions_mutual_by_resource (pypath.core.network.Network attribute) count_interactions_negative (pypath.core.network.Network attribute) count_interactions_negative() (pypath.core.interaction.Interaction method) count_interactions_negative_by_data_model (pypath.core.network.Network attribute) count_interactions_negative_by_interaction_type (pypath.core.network.Network attribute) count_interactions_negative_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interactions_negative_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interactions_negative_by_reference (pypath.core.network.Network attribute) count_interactions_negative_by_resource (pypath.core.network.Network attribute) count_interactions_non_directed (pypath.core.network.Network attribute) count_interactions_non_directed() (pypath.core.interaction.Interaction method) count_interactions_non_directed_0 (pypath.core.network.Network attribute) count_interactions_non_directed_0_by_data_model (pypath.core.network.Network attribute) count_interactions_non_directed_0_by_interaction_type (pypath.core.network.Network attribute) count_interactions_non_directed_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interactions_non_directed_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interactions_non_directed_0_by_reference (pypath.core.network.Network attribute) count_interactions_non_directed_0_by_resource (pypath.core.network.Network attribute) count_interactions_non_directed_by_data_model (pypath.core.network.Network attribute) count_interactions_non_directed_by_interaction_type (pypath.core.network.Network attribute) count_interactions_non_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interactions_non_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interactions_non_directed_by_reference (pypath.core.network.Network attribute) count_interactions_non_directed_by_resource (pypath.core.network.Network attribute) count_interactions_positive (pypath.core.network.Network attribute) count_interactions_positive() (pypath.core.interaction.Interaction method) count_interactions_positive_by_data_model (pypath.core.network.Network attribute) count_interactions_positive_by_interaction_type (pypath.core.network.Network attribute) count_interactions_positive_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interactions_positive_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interactions_positive_by_reference (pypath.core.network.Network attribute) count_interactions_positive_by_resource (pypath.core.network.Network attribute) count_interactions_signed (pypath.core.network.Network attribute) count_interactions_signed() (pypath.core.interaction.Interaction method) count_interactions_signed_by_data_model (pypath.core.network.Network attribute) count_interactions_signed_by_interaction_type (pypath.core.network.Network attribute) count_interactions_signed_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interactions_signed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interactions_signed_by_reference (pypath.core.network.Network attribute) count_interactions_signed_by_resource (pypath.core.network.Network attribute) count_interactions_undirected (pypath.core.network.Network attribute) count_interactions_undirected() (pypath.core.interaction.Interaction method) count_interactions_undirected_0 (pypath.core.network.Network attribute) count_interactions_undirected_0_by_data_model (pypath.core.network.Network attribute) count_interactions_undirected_0_by_interaction_type (pypath.core.network.Network attribute) count_interactions_undirected_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interactions_undirected_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interactions_undirected_0_by_reference (pypath.core.network.Network attribute) count_interactions_undirected_0_by_resource (pypath.core.network.Network attribute) count_interactions_undirected_by_data_model (pypath.core.network.Network attribute) count_interactions_undirected_by_interaction_type (pypath.core.network.Network attribute) count_interactions_undirected_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_interactions_undirected_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_interactions_undirected_by_reference (pypath.core.network.Network attribute) count_interactions_undirected_by_resource (pypath.core.network.Network attribute) count_labels (pypath.core.network.Network attribute) count_labels() (pypath.core.interaction.Interaction method) count_labels_by_data_model (pypath.core.network.Network attribute) count_labels_by_interaction_type (pypath.core.network.Network attribute) count_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_labels_by_reference (pypath.core.network.Network attribute) count_labels_by_resource (pypath.core.network.Network attribute) count_lncrna_identifiers (pypath.core.network.Network attribute) count_lncrna_identifiers() (pypath.core.interaction.Interaction method) count_lncrna_identifiers_by_data_model (pypath.core.network.Network attribute) count_lncrna_identifiers_by_interaction_type (pypath.core.network.Network attribute) count_lncrna_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_lncrna_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_lncrna_identifiers_by_reference (pypath.core.network.Network attribute) count_lncrna_identifiers_by_resource (pypath.core.network.Network attribute) count_lncrna_labels (pypath.core.network.Network attribute) count_lncrna_labels() (pypath.core.interaction.Interaction method) count_lncrna_labels_by_data_model (pypath.core.network.Network attribute) count_lncrna_labels_by_interaction_type (pypath.core.network.Network attribute) count_lncrna_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_lncrna_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_lncrna_labels_by_reference (pypath.core.network.Network attribute) count_lncrna_labels_by_resource (pypath.core.network.Network attribute) count_lncrnas (pypath.core.network.Network attribute) count_lncrnas() (pypath.core.interaction.Interaction method) count_lncrnas_by_data_model (pypath.core.network.Network attribute) count_lncrnas_by_interaction_type (pypath.core.network.Network attribute) count_lncrnas_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_lncrnas_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_lncrnas_by_reference (pypath.core.network.Network attribute) count_lncrnas_by_resource (pypath.core.network.Network attribute) count_mirna_identifiers (pypath.core.network.Network attribute) count_mirna_identifiers() (pypath.core.interaction.Interaction method) count_mirna_identifiers_by_data_model (pypath.core.network.Network attribute) count_mirna_identifiers_by_interaction_type (pypath.core.network.Network attribute) count_mirna_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_mirna_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_mirna_identifiers_by_reference (pypath.core.network.Network attribute) count_mirna_identifiers_by_resource (pypath.core.network.Network attribute) count_mirna_labels (pypath.core.network.Network attribute) count_mirna_labels() (pypath.core.interaction.Interaction method) count_mirna_labels_by_data_model (pypath.core.network.Network attribute) count_mirna_labels_by_interaction_type (pypath.core.network.Network attribute) count_mirna_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_mirna_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_mirna_labels_by_reference (pypath.core.network.Network attribute) count_mirna_labels_by_resource (pypath.core.network.Network attribute) count_mirnas (pypath.core.network.Network attribute) count_mirnas() (pypath.core.interaction.Interaction method) count_mirnas_by_data_model (pypath.core.network.Network attribute) count_mirnas_by_interaction_type (pypath.core.network.Network attribute) count_mirnas_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_mirnas_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_mirnas_by_reference (pypath.core.network.Network attribute) count_mirnas_by_resource (pypath.core.network.Network attribute) count_partners() (pypath.core.network.Network method) count_post_transcriptionally_activated_by (pypath.core.network.Network attribute) count_post_transcriptionally_activates (pypath.core.network.Network attribute) count_post_transcriptionally_regulated_by (pypath.core.network.Network attribute) count_post_transcriptionally_regulates (pypath.core.network.Network attribute) count_post_transcriptionally_suppressed_by (pypath.core.network.Network attribute) count_post_transcriptionally_suppresses (pypath.core.network.Network attribute) count_post_translationally_activated_by (pypath.core.network.Network attribute) count_post_translationally_activates (pypath.core.network.Network attribute) count_post_translationally_regulated_by (pypath.core.network.Network attribute) count_post_translationally_regulates (pypath.core.network.Network attribute) count_post_translationally_suppressed_by (pypath.core.network.Network attribute) count_post_translationally_suppresses (pypath.core.network.Network attribute) count_protein_identifiers (pypath.core.network.Network attribute) count_protein_identifiers() (pypath.core.interaction.Interaction method) count_protein_identifiers_by_data_model (pypath.core.network.Network attribute) count_protein_identifiers_by_interaction_type (pypath.core.network.Network attribute) count_protein_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_protein_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_protein_identifiers_by_reference (pypath.core.network.Network attribute) count_protein_identifiers_by_resource (pypath.core.network.Network attribute) count_protein_labels (pypath.core.network.Network attribute) count_protein_labels() (pypath.core.interaction.Interaction method) count_protein_labels_by_data_model (pypath.core.network.Network attribute) count_protein_labels_by_interaction_type (pypath.core.network.Network attribute) count_protein_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_protein_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_protein_labels_by_reference (pypath.core.network.Network attribute) count_protein_labels_by_resource (pypath.core.network.Network attribute) count_proteins (pypath.core.network.Network attribute) count_proteins() (pypath.core.interaction.Interaction method) count_proteins_by_data_model (pypath.core.network.Network attribute) count_proteins_by_interaction_type (pypath.core.network.Network attribute) count_proteins_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_proteins_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_proteins_by_reference (pypath.core.network.Network attribute) count_proteins_by_resource (pypath.core.network.Network attribute) count_references (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_references_by_data_model (pypath.core.network.Network attribute) count_references_by_interaction_type (pypath.core.network.Network attribute) count_references_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_references_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_references_by_reference (pypath.core.network.Network attribute) count_references_by_resource (pypath.core.network.Network attribute) count_regulated_by (pypath.core.network.Network attribute) count_regulates (pypath.core.network.Network attribute) count_resource_names (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_resource_names_by_data_model (pypath.core.network.Network attribute) count_resource_names_by_interaction_type (pypath.core.network.Network attribute) count_resource_names_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_resource_names_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_resource_names_by_reference (pypath.core.network.Network attribute) count_resource_names_by_resource (pypath.core.network.Network attribute) count_resource_names_via (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_resource_names_via_by_data_model (pypath.core.network.Network attribute) count_resource_names_via_by_interaction_type (pypath.core.network.Network attribute) count_resource_names_via_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_resource_names_via_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_resource_names_via_by_reference (pypath.core.network.Network attribute) count_resource_names_via_by_resource (pypath.core.network.Network attribute) count_resources (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_resources_by_data_model (pypath.core.network.Network attribute) count_resources_by_interaction_type (pypath.core.network.Network attribute) count_resources_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_resources_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_resources_by_reference (pypath.core.network.Network attribute) count_resources_by_resource (pypath.core.network.Network attribute) count_resources_via (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) count_resources_via_by_data_model (pypath.core.network.Network attribute) count_resources_via_by_interaction_type (pypath.core.network.Network attribute) count_resources_via_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_resources_via_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_resources_via_by_reference (pypath.core.network.Network attribute) count_resources_via_by_resource (pypath.core.network.Network attribute) count_small_molecule_identifiers (pypath.core.network.Network attribute) count_small_molecule_identifiers() (pypath.core.interaction.Interaction method) count_small_molecule_identifiers_by_data_model (pypath.core.network.Network attribute) count_small_molecule_identifiers_by_interaction_type (pypath.core.network.Network attribute) count_small_molecule_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_small_molecule_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_small_molecule_identifiers_by_reference (pypath.core.network.Network attribute) count_small_molecule_identifiers_by_resource (pypath.core.network.Network attribute) count_small_molecule_labels (pypath.core.network.Network attribute) count_small_molecule_labels() (pypath.core.interaction.Interaction method) count_small_molecule_labels_by_data_model (pypath.core.network.Network attribute) count_small_molecule_labels_by_interaction_type (pypath.core.network.Network attribute) count_small_molecule_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_small_molecule_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_small_molecule_labels_by_reference (pypath.core.network.Network attribute) count_small_molecule_labels_by_resource (pypath.core.network.Network attribute) count_small_molecules (pypath.core.network.Network attribute) count_small_molecules() (pypath.core.interaction.Interaction method) count_small_molecules_by_data_model (pypath.core.network.Network attribute) count_small_molecules_by_interaction_type (pypath.core.network.Network attribute) count_small_molecules_by_interaction_type_and_data_model (pypath.core.network.Network attribute) count_small_molecules_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) count_small_molecules_by_reference (pypath.core.network.Network attribute) count_small_molecules_by_resource (pypath.core.network.Network attribute) count_suppressed_by (pypath.core.network.Network attribute) count_suppresses (pypath.core.network.Network attribute) count_transcriptionally_activated_by (pypath.core.network.Network attribute) count_transcriptionally_activates (pypath.core.network.Network attribute) count_transcriptionally_regulated_by (pypath.core.network.Network attribute) count_transcriptionally_regulates (pypath.core.network.Network attribute) count_transcriptionally_suppressed_by (pypath.core.network.Network attribute) count_transcriptionally_suppresses (pypath.core.network.Network attribute) counts() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) counts_by_class() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) coverage() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) Cpad (class in pypath.core.annot) cpad_annotations() (in module pypath.inputs.cpad) cpad_pathway_cancer() (in module pypath.inputs.cpad) cpdb_interactions() (in module pypath.inputs.cpdb) cpdb_interactions_ltp() (in module pypath.inputs.cpdb) create_class() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) create_reverse() (pypath.utils.mapping.Mapper method) credentials() (in module pypath.inputs.credentials) cspa_annotations() (in module pypath.inputs.cspa) cspa_cell_type_annotations() (in module pypath.inputs.cspa) cspa_cell_types() (in module pypath.inputs.cspa) csv_sep_change() (in module pypath.inputs.common) ctdbase_relations() (in module pypath.inputs.ctdbase) ctdbase_vocabulary() (in module pypath.inputs.ctdbase) cui_interactions() (in module pypath.inputs.wang) curated (pypath.inputs.dorothea.DorotheaInteraction attribute) curated_ppi_resources() (in module pypath.omnipath.param) curated_sources (pypath.inputs.dorothea.DorotheaInteraction attribute) curation_effort() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) curation_effort_by_data_model (pypath.core.network.Network attribute) curation_effort_by_interaction_type (pypath.core.network.Network attribute) curation_effort_by_interaction_type_and_data_model (pypath.core.network.Network attribute) curation_effort_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) curation_effort_by_reference (pypath.core.network.Network attribute) curation_effort_by_resource (pypath.core.network.Network attribute) Curl (class in pypath.share.curl) CustomAnnotation (class in pypath.core.annot) Cytosig (class in pypath.core.annot) cytosig_annotations() (in module pypath.inputs.cytosig) cytosig_df() (in module pypath.inputs.cytosig)

D

DarkToLightEdgeDrawer (class in pypath.visual.igraph_drawing.edge) data_model (pypath.internals.resource.NetworkResourceKey attribute) data_models_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) data_models_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) data_models_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) data_models_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) data_models_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) data_models_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) data_type (pypath.internals.resource.EnzymeSubstrateResourceKey attribute) (pypath.internals.resource.NetworkResourceKey attribute) database (pypath.inputs.uniprot.UniprotRecordHistory attribute) DatabaseClass (class in pypath.omnipath.databases.define) DatabaseDefinition (class in pypath.omnipath.databases.define) DatabaseDefinitionManager (class in pypath.omnipath.databases.define) DatabaseManager (class in pypath.omnipath.app) databases (pypath.utils.uniprot.UniprotProtein property) databases() (in module pypath.utils.uniprot) dataset_dependencies() (pypath.omnipath.app.DatabaseManager method) datasets (pypath.core.evidence.Evidences property) datasets_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) datasets_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) datasets_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) datasets_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) datasets_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) datasets_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) date (pypath.inputs.uniprot.UniprotRecordHistory attribute) dbptm_enzyme_substrate() (in module pypath.inputs.dbptm) dbptm_enzyme_substrate_old() (in module pypath.inputs.dbptm) dbptm_interactions() (in module pypath.inputs.dbptm) ddinter_drug_interactions() (in module pypath.inputs.ddinter) ddinter_identifiers() (in module pypath.inputs.ddinter) ddinter_interactions() (in module pypath.inputs.ddinter) ddinter_mappings() (in module pypath.inputs.ddinter) ddinter_n_drugs() (in module pypath.inputs.ddinter) deathdomain_interactions() (in module pypath.inputs.deathdomain) deathdomain_interactions_rescued() (in module pypath.inputs.deathdomain) debug_off (class in pypath.share.curl) debug_on (class in pypath.share.curl) DefaultGraphDrawerFFsupport (class in pypath.visual.igraph_drawing) DefaultVertexDrawer (class in pypath.visual.igraph_drawing.vertex) (in module pypath.visual.igraph_drawing) define_dataset() (pypath.omnipath.app.DatabaseManager method) degree_inter_class_network() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) degrees_directed_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_in_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_in_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_in_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_in_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_in_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_in_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_out_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_out_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_out_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_out_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_out_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_directed_out_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_in_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_in_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_in_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_in_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_in_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_in_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_out_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_out_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_out_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_out_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_out_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_negative_out_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_non_directed_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_non_directed_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_non_directed_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_non_directed_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_non_directed_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_non_directed_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_in_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_in_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute)

degrees_positive_in_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_in_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_in_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_in_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_out_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_out_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_out_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_out_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_out_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_positive_out_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_in_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_in_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_in_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_in_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_in_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_in_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_out_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_out_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_out_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_out_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_out_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_signed_out_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_undirected_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_undirected_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_undirected_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_undirected_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_undirected_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) degrees_undirected_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) deleted_uniprot_genesymbol() (in module pypath.inputs.uniprot) depod_enzyme_substrate() (in module pypath.inputs.depod) depod_interactions() (in module pypath.inputs.depod) df() (pypath.utils.orthology.EnsemblOrthology method) (pypath.utils.orthology.HomologeneOrthology method) (pypath.utils.orthology.OmaOrthology method) (pypath.utils.orthology.ProteinOrthology method) Dgidb (class in pypath.core.annot) dgidb_annotations() (in module pypath.inputs.dgidb) dgidb_interactions() (in module pypath.inputs.dgidb) dip_interactions() (in module pypath.inputs.dip) dip_login() (in module pypath.inputs.dip) directed (pypath.core.interaction.InteractionDataFrameRecord attribute) direction_consistency() (pypath.core.network.Network method) direction_key() (pypath.core.interaction.Interaction method) disclaimer() (in module pypath) disease (pypath.inputs.pathophenodb.DiseasePathogen attribute) disease() (in module pypath.utils.uniprot) disease_id (pypath.inputs.pathophenodb.DiseasePathogen attribute) disease_pathogen_interactions() (in module pypath.inputs.pathophenodb) disease_to_drug() (in module pypath.inputs.kegg_api) disease_to_gene() (in module pypath.inputs.kegg_api) disease_to_pathway() (in module pypath.inputs.kegg_api) disease_with_xrefs() (in module pypath.utils.uniprot) DiseasePathogen (class in pypath.inputs.pathophenodb) diseases_general() (in module pypath.inputs.diseases) Disgenet (class in pypath.core.annot) dmodel (pypath.core.interaction.InteractionDataFrameRecord attribute) Domain (class in pypath.internals.intera) DomainDomain (class in pypath.internals.intera) DomainMotif (class in pypath.internals.intera) domino_ddi() (in module pypath.inputs.domino) domino_enzsub() (in module pypath.inputs.domino) domino_interactions() (in module pypath.inputs.domino) dorothea() (pypath.core.network.Network class method) dorothea_full_raw() (in module pypath.inputs.dorothea) dorothea_interactions() (in module pypath.inputs.dorothea) dorothea_interactions_old() (in module pypath.inputs.dorothea) dorothea_level() (pypath.core.interaction.Interaction method) dorothea_levels() (pypath.core.interaction.Interaction method) dorothea_old_csv() (in module pypath.inputs.dorothea) dorothea_rda_raw() (in module pypath.inputs.dorothea) DorotheaInteraction (class in pypath.inputs.dorothea) download_single_model() (in module pypath.inputs.biomodels) draw() (pypath.visual.drawing.InterSet method) (pypath.visual.igraph_drawing.vertex.AbstractCairoVertexDrawer method) (pypath.visual.igraph_drawing.vertex.AbstractVertexDrawer method) (pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer method) draw_directed_edge() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method) (pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method) (pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method) (pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method) (pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method) (pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method) draw_loop_edge() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method) (pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method) (pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method) (pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method) (pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method) (pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method) draw_undirected_edge() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method) (pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method) (pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method) (pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method) (pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method) (pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method) drug (pypath.inputs.adrecs.AdrecsDrug attribute) (pypath.inputs.adrecs.AdrecsDrugAdr attribute) drug_badd (pypath.inputs.adrecs.AdrecsDrugAdr attribute) drug_to_disease() (in module pypath.inputs.kegg_api) drug_to_drug() (in module pypath.inputs.kegg_api) drug_to_gene() (in module pypath.inputs.kegg_api) drug_to_pathway() (in module pypath.inputs.kegg_api) drugbank (pypath.inputs.adrecs.AdrecsDrug attribute) drugbank_annotations() (in module pypath.inputs.drugbank) drugbank_drugs() (in module pypath.inputs.drugbank) drugbank_drugs_full() (pypath.inputs.drugbank.DrugbankFull method) drugbank_external_ids_full() (pypath.inputs.drugbank.DrugbankFull method) drugbank_interactions() (in module pypath.inputs.drugbank) drugbank_mapping() (in module pypath.inputs.drugbank) drugbank_properties_full() (pypath.inputs.drugbank.DrugbankFull method) drugbank_raw_interactions() (in module pypath.inputs.drugbank) drugbank_targets_full() (pypath.inputs.drugbank.DrugbankFull method) DrugbankFull (class in pypath.inputs.drugbank) drugcentral_drugs() (in module pypath.inputs.drugcentral) drugcentral_interactions() (in module pypath.inputs.drugcentral) drugcentral_mapping() (in module pypath.inputs.drugcentral) dryrun_off (class in pypath.share.curl) dryrun_on (class in pypath.share.curl)

E

ebi_rest() (in module pypath.inputs.ebi) ec() (in module pypath.utils.uniprot) effect (pypath.core.interaction.InteractionDataFrameRecord attribute) (pypath.inputs.dorothea.DorotheaInteraction attribute) (pypath.inputs.gutmgene.GutmgeneAnnotation attribute) (pypath.inputs.gutmgene.GutmgeneRaw attribute) elm_classes() (in module pypath.inputs.elm) elm_domains() (in module pypath.inputs.elm) elm_instances() (in module pypath.inputs.elm) elm_interactions() (in module pypath.inputs.elm) embopress_supplementary() (in module pypath.inputs.embopress) Embrace (class in pypath.core.annot) embrace_annotations() (in module pypath.inputs.embrace) embrace_interactions() (in module pypath.inputs.embrace) embrace_raw() (in module pypath.inputs.embrace) embrace_translated() (in module pypath.inputs.embrace) enabled (pypath.internals.annot_formats.AnnotDef attribute) enables() (pypath.internals.license.License method) encode_tf_mirna_interactions() (in module pypath.inputs.encode) english (pypath.inputs.uniprot.Taxon attribute) ensembl_organisms() (in module pypath.inputs.ensembl) EnsemblOrtholog (class in pypath.utils.orthology) EnsemblOrthology (class in pypath.utils.orthology) ensure_common_name() (in module pypath.utils.taxonomy) ensure_dataset() (pypath.omnipath.app.DatabaseManager method) ensure_dirs() (pypath.omnipath.app.DatabaseManager method) ensure_ensembl_name() (in module pypath.utils.taxonomy) ensure_latin_name() (in module pypath.utils.taxonomy) ensure_module() (pypath.omnipath.app.DatabaseManager method) ensure_ncbi_tax_id() (in module pypath.utils.taxonomy) entities_by_data_model (pypath.core.network.Network attribute) entities_by_data_model() (pypath.core.interaction.Interaction method) entities_by_interaction_type (pypath.core.network.Network attribute) entities_by_interaction_type() (pypath.core.interaction.Interaction method) entities_by_interaction_type_and_data_model (pypath.core.network.Network attribute) entities_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) entities_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) entities_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) entities_by_reference (pypath.core.network.Network attribute) entities_by_reference() (pypath.core.interaction.Interaction method) entities_by_resource (pypath.core.network.Network attribute) entities_by_resource() (pypath.core.interaction.Interaction method) Entity (class in pypath.core.entity) (class in pypath.utils.pyreact) entity_a (pypath.core.interaction.InteractionKey attribute) entity_b (pypath.core.interaction.InteractionKey attribute)

entity_by_id() (pypath.core.network.Network method) entity_by_label() (pypath.core.network.Network method) entity_type (pypath.core.entity.EntityKey attribute) EntityKey (class in pypath.core.entity) EntityList (class in pypath.core.entity) EntitySet (class in pypath.utils.pyreact) entrez (pypath.inputs.gutmgene.GutmgeneRaw attribute) entry_name (pypath.inputs.uniprot.UniprotRecordHistory attribute) entry_version (pypath.inputs.uniprot.UniprotRecordHistory attribute) enzyme (pypath.inputs.iptmnet.IptmnetInteraction attribute) enzyme_isoform (pypath.inputs.iptmnet.IptmnetInteraction attribute) enzyme_substrate (in module pypath.resources.data_formats) EnzymeSubstrateAggregator (class in pypath.core.enz_sub) EnzymeSubstrateOrthologyProcessor (class in pypath.core.enz_sub) EnzymeSubstrateProcessor (class in pypath.core.enz_sub) EnzymeSubstrateResource (class in pypath.internals.resource) EnzymeSubstrateResourceKey (class in pypath.internals.resource) esummary() (in module pypath.inputs.eutils) evaluate_evidences() (pypath.core.interaction.Interaction method) Evidence (class in pypath.core.evidence) evidence (pypath.inputs.pathophenodb.DiseasePathogen attribute) Evidences (class in pypath.core.evidence) evidences_by_data_model (pypath.core.network.Network attribute) evidences_by_interaction_type (pypath.core.network.Network attribute) evidences_by_interaction_type_and_data_model (pypath.core.network.Network attribute) evidences_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) evidences_by_reference (pypath.core.network.Network attribute) evidences_by_resource (pypath.core.network.Network attribute) exclude (pypath.internals.annot_formats.AnnotDef attribute) excludes (in module pypath.core.intercell_annot) Exocarta (class in pypath.core.annot) expand() (pypath.utils.pyreact.Entity method) (pypath.utils.pyreact.Protein method) (pypath.utils.pyreact.ReactionSide method) (pypath.utils.pyreact.Reference method) expasy_enzyme_classes() (in module pypath.inputs.expasy) expasy_enzymes() (in module pypath.inputs.expasy) experiments_filtered() (in module pypath.inputs.diseases) experiments_full() (in module pypath.inputs.diseases) Export (class in pypath.omnipath.export) export_licenses() (in module pypath.omnipath.server.generate_about_page) (in module pypath.resources.descriptions) expr_names_to_terms() (pypath.utils.go.GOAnnotation method) extra_directions() (pypath.core.network.Network method) extract() (pypath.share.curl.Curl method) (pypath.share.curl.FileOpener method) (pypath.utils.pyreact.BioPaxReader method)

F

fail_on_empty (pypath.inputs.uniprot.UniprotQuery attribute) family (pypath.inputs.icellnet.IcellnetRecord attribute) features_table() (in module pypath.utils.uniprot) Field (class in pypath.inputs.hmdb.schema.common) FileMapping (class in pypath.internals.input_formats) FileOpener (class in pypath.share.curl) filter() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) filter_classes() (pypath.core.annot.CustomAnnotation static method) (pypath.core.intercell.IntercellAnnotation static method) filter_entity_type() (pypath.core.entity.Entity class method) (pypath.internals.annot_formats.AnnotationGroup method) filter_interclass_network() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) filter_network_df() (in module pypath.core.common)

find_paths() (pypath.core.network.Network method) findall() (pypath.utils.seq.Seq method) flatten() (pypath.utils.go.GeneOntology method) foreach_dataset() (pypath.omnipath.app.DatabaseManager method) frequency (pypath.inputs.sider.SiderSideeffetFrequency attribute) from_dict() (pypath.omnipath.databases.define.DatabaseDefinition class method) from_igraph() (pypath.core.network.Network class method) from_json() (pypath.omnipath.databases.define.DatabaseDefinition class method) from_pickle() (pypath.core.network.Network class method) full_name() (in module pypath.utils.uniprot) function() (in module pypath.utils.uniprot) function_genecards() (in module pypath.utils.uniprot) function_or_genecards() (in module pypath.utils.uniprot) function_with_genecards() (in module pypath.utils.uniprot) function_with_xrefs() (in module pypath.utils.uniprot)

G

gen_cvariations() (pypath.utils.pyreact.PyReact method) gen_html() (in module pypath.resources.descriptions) gene_to_disease() (in module pypath.inputs.kegg_api) gene_to_drug() (in module pypath.inputs.kegg_api) gene_to_pathway() (in module pypath.inputs.kegg_api) genecards_datasheet() (in module pypath.inputs.genecards) genecards_soup() (in module pypath.inputs.genecards) genecards_summaries() (in module pypath.inputs.genecards) GeneOntology (class in pypath.utils.go) generate_about_html() (in module pypath.omnipath.server.generate_about_page) generate_df_records() (pypath.core.interaction.Interaction method) generic_attr_processor() (pypath.omnipath.export.Export static method) genesymbol (pypath.inputs.gutmgene.GutmgeneRaw attribute) genesymbol() (in module pypath.utils.uniprot) get() (pypath.internals.resource.NetworkDataset method) get_3did() (in module pypath.inputs.threedid) get_3did_ddi() (in module pypath.inputs.threedid) get_3did_dmi() (in module pypath.inputs.threedid) get_acsn_effects() (in module pypath.inputs.reaction) get_all_ancestors() (pypath.utils.go.GeneOntology method) get_all_descendants() (pypath.utils.go.GeneOntology method) get_all_models() (in module pypath.inputs.biomodels) get_annot() (pypath.utils.go.GOAnnotation method) get_annot_ancestors() (pypath.utils.go.GOAnnotation method) get_annotation() (pypath.core.annot.GOCustomIntercell method) (pypath.utils.go.GOCustomAnnotation method) get_annotations() (pypath.core.annot.GOCustomIntercell method) (pypath.utils.go.GOCustomAnnotation method) get_annots() (pypath.utils.go.GOAnnotation method) get_annots_ancestors() (pypath.utils.go.GOAnnotation method) get_args_curated() (pypath.omnipath.app.DatabaseManager method) get_args_lncrna_mrna() (pypath.omnipath.app.DatabaseManager method) get_args_mirna_mrna() (pypath.omnipath.app.DatabaseManager method) get_args_small_molecule() (pypath.omnipath.app.DatabaseManager method) get_args_tf_mirna() (pypath.omnipath.app.DatabaseManager method) get_args_tf_target() (pypath.omnipath.app.DatabaseManager method) get_aspect() (pypath.utils.go.GeneOntology method) get_attr() (pypath.core.interaction.Interaction method) get_biomodels() (in module pypath.inputs.biomodels) get_biomodels_req() (in module pypath.inputs.biomodels) get_bonds() (pypath.internals.intera.Interface method) get_build_args() (pypath.omnipath.app.DatabaseManager method) get_cachedir() (in module pypath.share.cache) get_categories() (in module pypath.legacy.db_categories) get_category() (in module pypath.legacy.db_categories) get_class() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) get_complex_identifiers (pypath.core.network.Network attribute) get_complex_identifiers() (pypath.core.interaction.Interaction method) get_complex_labels (pypath.core.network.Network attribute) get_complex_labels() (pypath.core.interaction.Interaction method) get_complexes (pypath.core.network.Network attribute) get_complexes() (pypath.core.interaction.Interaction method) get_controller() (in module pypath.resources) get_controls() (in module pypath.inputs.reaction) get_cpad() (in module pypath.inputs.cpad) get_csa() (in module pypath.inputs.csa) get_curation_effort (pypath.core.network.Network attribute) get_data_models (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_datasets (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_db() (in module pypath.core.annot) (in module pypath.core.complex) (in module pypath.core.enz_sub) (in module pypath.core.intercell) (in module pypath.core.network) (in module pypath.inputs.uniprot_db) (in module pypath.utils.go) (in module pypath.utils.taxonomy) (pypath.omnipath.app.DatabaseManager method) get_degrees() (pypath.core.interaction.Interaction method) get_degrees_directed (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_directed_in (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_directed_out (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_negative (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_negative_in (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_negative_out (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_non_directed (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_positive (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_positive_in (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_positive_out (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_signed (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_signed_in (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_signed_out (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_degrees_undirected (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_desc() (pypath.share.progress.Progress method) get_df() (in module pypath.utils.orthology) (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) (pypath.utils.orthology.OrthologyManager method) get_dgidb_old() (in module pypath.inputs.dgidb) get_dict() (in module pypath.utils.orthology) (pypath.utils.orthology.OrthologyManager method) get_direction() (pypath.core.interaction.Interaction method) get_directions() (pypath.core.interaction.Interaction method) get_domino() (in module pypath.inputs.domino) get_dorothea_old() (in module pypath.inputs.dorothea) get_entities (pypath.core.network.Network attribute) get_entities() (pypath.core.interaction.Interaction method) get_evidences (pypath.core.network.Network attribute) get_exocarta() (in module pypath.inputs.exocarta) get_expression() (pypath.utils.proteomicsdb.ProteomicsDB method) get_go_desc() (in module pypath.inputs.go) get_go_quick() (in module pypath.inputs.go) get_goslim() (in module pypath.inputs.go) get_havugimana() (in module pypath.inputs.havugimana) get_header() (pypath.omnipath.export.Export method) get_homologene() (in module pypath.inputs.homologene) get_hpmr() (in module pypath.inputs.hpmr) get_hprd() (in module pypath.inputs.hprd) get_i3d() (in module pypath.inputs.i3d) get_identifiers (pypath.core.network.Network attribute) get_identifiers() (pypath.core.interaction.Interaction method) get_ielm() (in module pypath.inputs.ielm) get_ielm_huge() (in module pypath.inputs.ielm) get_imweb() (in module pypath.inputs.imweb) get_imweb_req() (in module pypath.inputs.imweb) get_instruct() (in module pypath.inputs.instruct) get_instruct_offsets() (in module pypath.inputs.instruct) get_integrins() (in module pypath.inputs.integrins) get_interaction_types (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_interactions (pypath.core.network.Network attribute) get_interactions() (in module pypath.inputs.reaction) (pypath.core.interaction.Interaction method) get_interactions_0 (pypath.core.network.Network attribute) get_interactions_0() (pypath.core.interaction.Interaction method) get_interactions_directed (pypath.core.network.Network attribute) get_interactions_directed() (pypath.core.interaction.Interaction method) get_interactions_mutual (pypath.core.network.Network attribute) get_interactions_mutual() (pypath.core.interaction.Interaction method) get_interactions_negative (pypath.core.network.Network attribute) get_interactions_negative() (pypath.core.interaction.Interaction method) get_interactions_non_directed (pypath.core.network.Network attribute) get_interactions_non_directed() (pypath.core.interaction.Interaction method) get_interactions_non_directed_0 (pypath.core.network.Network attribute) get_interactions_non_directed_0() (pypath.core.interaction.Interaction method) get_interactions_positive (pypath.core.network.Network attribute) get_interactions_positive() (pypath.core.interaction.Interaction method) get_interactions_signed (pypath.core.network.Network attribute) get_interactions_signed() (pypath.core.interaction.Interaction method) get_interactions_undirected (pypath.core.network.Network attribute) get_interactions_undirected() (pypath.core.interaction.Interaction method) get_interactions_undirected_0 (pypath.core.network.Network attribute) get_interactions_undirected_0() (pypath.core.interaction.Interaction method) get_interclass_network_df() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) get_isoforms() (in module pypath.utils.seq) get_key() (pypath.utils.mapping.MappingTable method) get_kinase_class() (in module pypath.inputs.mimp) get_label_position() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method) (pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method) (pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method) (pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method) (pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method) (pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method) get_labels (pypath.core.network.Network attribute) get_labels() (pypath.core.interaction.Interaction method) get_li2012() (in module pypath.inputs.li2012) get_line() (pypath.internals.intera.DomainMotif method) get_lncrna_identifiers (pypath.core.network.Network attribute) get_lncrna_identifiers() (pypath.core.interaction.Interaction method) get_lncrna_labels (pypath.core.network.Network attribute) get_lncrna_labels() (pypath.core.interaction.Interaction method) get_lncrnas (pypath.core.network.Network attribute) get_lncrnas() (pypath.core.interaction.Interaction method) get_manager() (in module pypath.omnipath.databases) (in module pypath.utils.orthology) (in module pypath.utils.reflists) get_mapper() (in module pypath.utils.mapping) get_method() (in module pypath.inputs) get_mirbase_aliases() (in module pypath.inputs.mirbase) get_mirna_identifiers (pypath.core.network.Network attribute) get_mirna_identifiers() (pypath.core.interaction.Interaction method) get_mirna_labels (pypath.core.network.Network attribute) get_mirna_labels() (pypath.core.interaction.Interaction method) get_mirnas (pypath.core.network.Network attribute) get_mirnas() (pypath.core.interaction.Interaction method) get_name() (pypath.utils.go.GeneOntology method) (pypath.utils.go.GOAnnotation method) get_names() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) get_organisms() (pypath.core.network.Network method) get_param() (pypath.omnipath.app.DatabaseManager method) get_parents() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) get_pieces() (pypath.utils.proteomicsdb.ProteomicsDB method) get_pmid() (in module pypath.inputs.pubmed) get_pro() (in module pypath.inputs.pro) get_protein_identifiers (pypath.core.network.Network attribute) get_protein_identifiers() (pypath.core.interaction.Interaction method) get_protein_labels (pypath.core.network.Network attribute) get_protein_labels() (pypath.core.interaction.Interaction method) get_proteinatlas() (in module pypath.inputs.proteinatlas) get_proteins (pypath.core.network.Network attribute) get_proteins() (pypath.core.interaction.Interaction method) (pypath.utils.proteomicsdb.ProteomicsDB method) get_protmapper() (in module pypath.inputs.protmapper) get_pubmed_data() (in module pypath.internals.refs) get_pubmeds() (in module pypath.inputs.pubmed) get_reactions() (in module pypath.inputs.reaction) get_reference_set() (pypath.core.annot.Adhesome static method) (pypath.core.annot.Almen2009 static method) (pypath.core.annot.AnnotationBase static method) (pypath.core.annot.Baccin2019 static method) (pypath.core.annot.Biogps static method) (pypath.core.annot.Cancerdrugsdb static method) (pypath.core.annot.CancerGeneCensus static method) (pypath.core.annot.Cancersea static method) (pypath.core.annot.Cellcall static method) (pypath.core.annot.Cellcellinteractions static method) (pypath.core.annot.Cellchatdb static method) (pypath.core.annot.CellchatdbComplex static method) (pypath.core.annot.Cellinker static method) (pypath.core.annot.CellinkerComplex static method) (pypath.core.annot.CellPhoneDB static method) (pypath.core.annot.CellPhoneDBComplex static method) (pypath.core.annot.CellSurfaceProteinAtlas static method) (pypath.core.annot.CellSurfaceProteinAtlasCellType static method) (pypath.core.annot.Celltalkdb static method) (pypath.core.annot.Celltypist static method) (pypath.core.annot.Comppi static method) (pypath.core.annot.Connectomedb static method) (pypath.core.annot.Corum static method) (pypath.core.annot.CorumFuncat static method) (pypath.core.annot.CorumGO static method) (pypath.core.annot.Cpad static method) (pypath.core.annot.Cytosig static method) (pypath.core.annot.Dgidb static method) (pypath.core.annot.Disgenet static method) (pypath.core.annot.Embrace static method) (pypath.core.annot.Exocarta static method) (pypath.core.annot.GOIntercell static method) (pypath.core.annot.Gpcrdb static method) (pypath.core.annot.GuideToPharmacology static method) (pypath.core.annot.Hgnc static method) (pypath.core.annot.HpmrComplex static method) (pypath.core.annot.HPO static method) (pypath.core.annot.Humancellmap static method) (pypath.core.annot.HumanPlasmaMembraneReceptome static method) (pypath.core.annot.HumanProteinAtlas static method) (pypath.core.annot.HumanProteinAtlasSecretome static method) (pypath.core.annot.HumanProteinAtlasSubcellular static method) (pypath.core.annot.Icellnet static method) (pypath.core.annot.IcellnetComplex static method) (pypath.core.annot.Integrins static method) (pypath.core.annot.InterPro static method) (pypath.core.annot.Intogen static method) (pypath.core.annot.Italk static method) (pypath.core.annot.KeggPathways static method) (pypath.core.annot.KeggPathwaysPC static method) (pypath.core.annot.Kinasedotcom static method) (pypath.core.annot.Kirouac2010 static method) (pypath.core.annot.Lambert2018 static method) (pypath.core.annot.LigandReceptor static method) (pypath.core.annot.Locate static method) (pypath.core.annot.Lrdb static method) (pypath.core.annot.Matrisome static method) (pypath.core.annot.Matrixdb static method) (pypath.core.annot.Mcam static method) (pypath.core.annot.Membranome static method) (pypath.core.annot.Msigdb static method) (pypath.core.annot.NetpathPathways static method) (pypath.core.annot.Opm static method) (pypath.core.annot.Panglaodb static method) (pypath.core.annot.Phobius static method) (pypath.core.annot.Phosphatome static method) (pypath.core.annot.Progeny static method) (pypath.core.annot.Ramilowski2015 static method) (pypath.core.annot.Ramilowski2015Location static method) (pypath.core.annot.Scconnect static method) (pypath.core.annot.ScconnectComplex static method) (pypath.core.annot.SignalinkFunctions static method) (pypath.core.annot.SignalinkPathways static method) (pypath.core.annot.SignorPathways static method) (pypath.core.annot.Surfaceome static method) (pypath.core.annot.Talklr static method) (pypath.core.annot.Tcdb static method) (pypath.core.annot.Tfcensus static method) (pypath.core.annot.Topdb static method) (pypath.core.annot.UniprotFamilies static method) (pypath.core.annot.UniprotKeywords static method) (pypath.core.annot.UniprotLocations static method) (pypath.core.annot.UniprotTissues static method) (pypath.core.annot.UniprotTopologies static method) (pypath.core.annot.Vesiclepedia static method) (pypath.core.annot.Wang static method) (pypath.core.annot.Zhong2015 static method)

get_references (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_reflist() (in module pypath.utils.reflists) get_residue() (pypath.utils.pdb.ResidueMapper method) get_resource() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) get_resource_names (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_resource_names_via (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_resources (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_resources() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) get_resources_via (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) get_sign() (pypath.core.interaction.Interaction method) get_single_model() (in module pypath.inputs.biomodels) get_small_molecule_identifiers (pypath.core.network.Network attribute) get_small_molecule_identifiers() (pypath.core.interaction.Interaction method) get_small_molecule_labels (pypath.core.network.Network attribute) get_small_molecule_labels() (pypath.core.interaction.Interaction method) get_small_molecules (pypath.core.network.Network attribute) get_small_molecules() (pypath.core.interaction.Interaction method) get_soup() (in module pypath.inputs.reaction) get_subset() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) get_subset_bool_array() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) get_switches_elm() (in module pypath.inputs.switches_elm) get_table_key() (pypath.utils.mapping.Mapper method) get_term() (pypath.utils.go.GeneOntology method) (pypath.utils.go.GOAnnotation method) get_tfregulons() (in module pypath.inputs.dorothea) get_tissues() (pypath.utils.proteomicsdb.ProteomicsDB method) get_uniprot_sec() (in module pypath.inputs.uniprot) get_values() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) get_vesiclepedia() (in module pypath.inputs.exocarta) get_via() (pypath.internals.resource.EnzymeSubstrateResource method) glom_fields() (in module pypath.inputs.common) go_ancestors() (in module pypath.inputs.go) go_ancestors_goose() (in module pypath.inputs.go) go_ancestors_quickgo() (in module pypath.inputs.go) go_annotations() (in module pypath.inputs.go) go_annotations_all() (in module pypath.inputs.go) go_annotations_goa() (in module pypath.inputs.go) go_annotations_goose() (in module pypath.inputs.go) go_annotations_quickgo() (in module pypath.inputs.go) go_annotations_solr() (in module pypath.inputs.go) go_annotations_uniprot() (in module pypath.inputs.go) go_descendants() (in module pypath.inputs.go) go_descendants_goose() (in module pypath.inputs.go) go_descendants_quickgo() (in module pypath.inputs.go) go_descendants_to_ancestors() (in module pypath.inputs.go) go_terms() (in module pypath.inputs.go) go_terms_goose() (in module pypath.inputs.go) go_terms_quickgo() (in module pypath.inputs.go) go_terms_solr() (in module pypath.inputs.go) GOAnnotation (class in pypath.utils.go) GOCustomAnnotation (class in pypath.utils.go) GOCustomIntercell (class in pypath.core.annot) GOIntercell (class in pypath.core.annot) Gpcrdb (class in pypath.core.annot) gpcrdb_annotations() (in module pypath.inputs.gpcrdb) graphviz_attrs() (in module pypath.inputs.graphviz) guess_type() (in module pypath.utils.mapping) (pypath.utils.mapping.Mapper method) guide2pharma_complexes() (in module pypath.inputs.guide2pharma) guide2pharma_download() (in module pypath.inputs.guide2pharma) guide2pharma_interactions() (in module pypath.inputs.guide2pharma) GuideToPharmacology (class in pypath.core.annot) (class in pypath.core.complex) gut_microbiota_id (pypath.inputs.gutmgene.GutmgeneAnnotation attribute) (pypath.inputs.gutmgene.GutmgeneRaw attribute) gutmgene_annotations() (in module pypath.inputs.gutmgene) gutmgene_raw() (in module pypath.inputs.gutmgene) GutmgeneAnnotation (class in pypath.inputs.gutmgene) GutmgeneRaw (class in pypath.inputs.gutmgene)

H

has_any_term() (pypath.utils.go.GOAnnotation method) has_dataset() (pypath.core.evidence.Evidences method) has_interaction_type() (pypath.core.evidence.Evidence method) (pypath.core.evidence.Evidences method) has_mapping_table() (pypath.utils.mapping.Mapper method) has_sign() (pypath.core.interaction.Interaction method) has_tag() (in module pypath.utils.uniprot) has_term() (pypath.utils.go.GOAnnotation method) Havugimana (class in pypath.core.complex) havugimana_complexes() (in module pypath.inputs.havugimana) hc (pypath.utils.orthology.EnsemblOrtholog attribute) Hgnc (class in pypath.core.annot) hgnc_genegroups() (in module pypath.inputs.hgnc) hi_i_interactions() (in module pypath.inputs.huri) hi_ii_interactions() (in module pypath.inputs.huri) hi_iii_old() (in module pypath.inputs.huri) hi_union_interactions() (in module pypath.inputs.huri) highest() (pypath.utils.go.GeneOntology method) hippie_interactions() (in module pypath.inputs.hippie) hmdb_xml() (in module pypath.inputs.hmdb.xml) HmdbMapping (class in pypath.internals.input_formats) homologene_dict() (in module pypath.inputs.homologene) homologene_uniprot_dict() (in module pypath.inputs.homologene) HomologeneOrtholog (class in pypath.utils.orthology) HomologeneOrthology (class in pypath.utils.orthology) Hpmr (class in pypath.core.complex) hpmr_annotations() (in module pypath.inputs.hpmr)

hpmr_complexes() (in module pypath.inputs.hpmr) hpmr_interactions() (in module pypath.inputs.hpmr) HpmrComplex (class in pypath.core.annot) HpmrInteraction (class in pypath.inputs.hpmr) HPO (class in pypath.core.annot) hpo_annotations() (in module pypath.inputs.hpo) hpo_diseases() (in module pypath.inputs.hpo) hpo_ontology() (in module pypath.inputs.hpo) hpo_terms() (in module pypath.inputs.hpo) hprd_enzyme_substrate() (in module pypath.inputs.hprd) hprd_interactions() (in module pypath.inputs.hprd) hprd_interactions_htp() (in module pypath.inputs.hprd) hsn_interactions() (in module pypath.inputs.wang) htp_interactions() (pypath.core.network.Network method) htp_references() (pypath.core.network.Network method) htri_interactions() (in module pypath.inputs.htri) Humancellmap (class in pypath.core.annot) humancellmap_annotations() (in module pypath.inputs.humancellmap) HumanPlasmaMembraneReceptome (class in pypath.core.annot) HumanProteinAtlas (class in pypath.core.annot) HumanProteinAtlasSecretome (class in pypath.core.annot) HumanProteinAtlasSubcellular (class in pypath.core.annot) Humap (class in pypath.core.complex) Humap2 (class in pypath.core.complex) humap2_complexes() (in module pypath.inputs.humap) humap_complexes() (in module pypath.inputs.humap) huri_interactions() (in module pypath.inputs.huri)

I

i_select_by_term() (pypath.utils.go.GOAnnotation method) Icellnet (class in pypath.core.annot) (class in pypath.core.complex) icellnet_annotations() (in module pypath.inputs.icellnet) icellnet_complexes() (in module pypath.inputs.icellnet) icellnet_interactions() (in module pypath.inputs.icellnet) IcellnetComplex (class in pypath.core.annot) IcellnetRecord (class in pypath.inputs.icellnet) id (pypath.utils.orthology.EnsemblOrtholog attribute) (pypath.utils.orthology.HomologeneOrtholog attribute) (pypath.utils.orthology.OmaOrtholog attribute) id() (in module pypath.utils.uniprot) id_a (pypath.core.interaction.InteractionDataFrameRecord attribute) (pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute) id_b (pypath.core.interaction.InteractionDataFrameRecord attribute) (pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute) id_from_label() (in module pypath.utils.mapping) id_from_label0() (in module pypath.utils.mapping) id_type (pypath.core.entity.EntityKey attribute) (pypath.utils.mapping.MappingTableKey attribute) (pypath.utils.orthology.OrthologyTableKey attribute) id_type_side() (pypath.utils.mapping.MapReader method) id_types() (in module pypath.utils.mapping) (pypath.utils.mapping.Mapper class method) identifier (pypath.core.entity.EntityKey attribute) identifier() (pypath.utils.mapping.Mapper method) identifiers_by_data_model (pypath.core.network.Network attribute) identifiers_by_data_model() (pypath.core.interaction.Interaction method) identifiers_by_interaction_type (pypath.core.network.Network attribute) identifiers_by_interaction_type() (pypath.core.interaction.Interaction method) identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) identifiers_by_reference (pypath.core.network.Network attribute) identifiers_by_reference() (pypath.core.interaction.Interaction method) identifiers_by_resource (pypath.core.network.Network attribute) identifiers_by_resource() (pypath.core.interaction.Interaction method) idtypes() (in module pypath.inputs.uniprot_idmapping) ignore_pandas_copywarn() (in module pypath.omnipath.server.run) in_same_component() (pypath.utils.pyreact.PyReact method) inchikey2anything() (pypath.utils.unichem.Unichem method) index() (pypath.core.entity.EntityKey method) (pypath.core.interaction.InteractionDataFrameRecord method) (pypath.core.interaction.InteractionKey method) (pypath.core.network.NetworkStatsRecord method) (pypath.inputs.adrecs.AdrecsAdr method) (pypath.inputs.adrecs.AdrecsChildParent method) (pypath.inputs.adrecs.AdrecsDrug method) (pypath.inputs.adrecs.AdrecsDrugAdr method) (pypath.inputs.adrecs.AdrecsTerm method) (pypath.inputs.biogps.BiogpsDataset method) (pypath.inputs.cellinker.CellinkerInteraction method) (pypath.inputs.cellphonedb.CellPhoneDBAnnotation method) (pypath.inputs.dorothea.DorotheaInteraction method) (pypath.inputs.gutmgene.GutmgeneAnnotation method) (pypath.inputs.gutmgene.GutmgeneRaw method) (pypath.inputs.hpmr.HpmrInteraction method) (pypath.inputs.icellnet.IcellnetRecord method) (pypath.inputs.iptmnet.IptmnetInteraction method) (pypath.inputs.kegg.KeggPathway method) (pypath.inputs.lrdb.LrdbAnnotation method) (pypath.inputs.pathophenodb.DiseasePathogen method) (pypath.inputs.pathwaycommons.PathwayCommonsInteraction method) (pypath.inputs.pathwaycommons.PathwayCommonsResource method) (pypath.inputs.pisa.PisaBond method) (pypath.inputs.sider.SiderDrug method) (pypath.inputs.sider.SiderSideeffect method) (pypath.inputs.sider.SiderSideeffectMeddra method) (pypath.inputs.sider.SiderSideeffetFrequency method) (pypath.inputs.uniprot.Taxon method) (pypath.inputs.uniprot.UniprotRecordHistory method) (pypath.internals.annot_formats.AnnotDef method) (pypath.internals.annot_formats.AnnotDefKey method) (pypath.internals.annot_formats.AnnotOp method) (pypath.internals.resource.EnzymeSubstrateResourceKey method) (pypath.internals.resource.NetworkResourceKey method) (pypath.utils.mapping.MappingTableKey method) (pypath.utils.orthology.EnsemblOrtholog method) (pypath.utils.orthology.HomologeneOrtholog method) (pypath.utils.orthology.OmaOrtholog method) (pypath.utils.orthology.OrthologyTableKey method) (pypath.utils.pdb.Residue method) (pypath.utils.pdb.Segment method) info() (in module pypath) (in module pypath.inputs.unichem) (in module pypath.utils.uniprot) (pypath.utils.unichem.Unichem static method) info_section() (in module pypath.utils.uniprot) (pypath.utils.uniprot.UniprotProtein method) init() (in module pypath.omnipath) (in module pypath.utils.mapping) (in module pypath.utils.orthology) (in module pypath.utils.reflists) init_db() (in module pypath.core.annot) (in module pypath.core.complex) (in module pypath.core.enz_sub) (in module pypath.core.intercell) (in module pypath.core.network) (in module pypath.inputs.uniprot_db) (in module pypath.utils.go) (in module pypath.utils.taxonomy) init_etree() (pypath.utils.pyreact.BioPaxReader method) init_manager() (in module pypath.omnipath.databases) init_network() (pypath.core.network.Network method) init_tqdm() (pypath.share.progress.Progress method) innatedb_interactions() (in module pypath.inputs.innatedb) int_to_level() (pypath.internals.license.LicenseAttrib class method) (pypath.internals.license.LicenseFeature class method) (pypath.internals.license.LicensePurpose class method) (pypath.internals.license.LicenseSharing class method) intact_interactions() (in module pypath.inputs.intact) integrin (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute) Integrins (class in pypath.core.annot) Interaction (class in pypath.core.interaction) interaction (in module pypath.resources.data_formats) interaction() (in module pypath.utils.uniprot) (pypath.core.network.Network method) interaction_by_id() (pypath.core.network.Network method) interaction_by_label() (pypath.core.network.Network method) interaction_htp (in module pypath.resources.data_formats) interaction_type (pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute) (pypath.internals.resource.NetworkResourceKey attribute) interaction_types_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) interaction_types_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) interaction_types_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) interaction_types_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) interaction_types_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) interaction_types_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) interaction_with_xrefs() (in module pypath.utils.uniprot) InteractionDataFrameRecord (class in pypath.core.interaction) InteractionKey (class in pypath.core.interaction) interactions_0_by_data_model (pypath.core.network.Network attribute) interactions_0_by_data_model() (pypath.core.interaction.Interaction method) interactions_0_by_interaction_type (pypath.core.network.Network attribute) interactions_0_by_interaction_type() (pypath.core.interaction.Interaction method) interactions_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute) interactions_0_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) interactions_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) interactions_0_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) interactions_0_by_reference (pypath.core.network.Network attribute) interactions_0_by_reference() (pypath.core.interaction.Interaction method) interactions_0_by_resource (pypath.core.network.Network attribute) interactions_0_by_resource() (pypath.core.interaction.Interaction method) interactions_by_data_model (pypath.core.network.Network attribute) interactions_by_data_model() (pypath.core.interaction.Interaction method) interactions_by_interaction_type (pypath.core.network.Network attribute) interactions_by_interaction_type() (pypath.core.interaction.Interaction method) interactions_by_interaction_type_and_data_model (pypath.core.network.Network attribute) interactions_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) interactions_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) interactions_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) interactions_by_reference (pypath.core.network.Network attribute) interactions_by_reference() (pypath.core.interaction.Interaction method) interactions_by_resource (pypath.core.network.Network attribute)

interactions_by_resource() (pypath.core.interaction.Interaction method) interactions_directed_by_data_model (pypath.core.network.Network attribute) interactions_directed_by_data_model() (pypath.core.interaction.Interaction method) interactions_directed_by_interaction_type (pypath.core.network.Network attribute) interactions_directed_by_interaction_type() (pypath.core.interaction.Interaction method) interactions_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute) interactions_directed_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) interactions_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) interactions_directed_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) interactions_directed_by_reference (pypath.core.network.Network attribute) interactions_directed_by_reference() (pypath.core.interaction.Interaction method) interactions_directed_by_resource (pypath.core.network.Network attribute) interactions_directed_by_resource() (pypath.core.interaction.Interaction method) interactions_mutual_by_data_model (pypath.core.network.Network attribute) interactions_mutual_by_data_model() (pypath.core.interaction.Interaction method) interactions_mutual_by_interaction_type (pypath.core.network.Network attribute) interactions_mutual_by_interaction_type() (pypath.core.interaction.Interaction method) interactions_mutual_by_interaction_type_and_data_model (pypath.core.network.Network attribute) interactions_mutual_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) interactions_mutual_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) interactions_mutual_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) interactions_mutual_by_reference (pypath.core.network.Network attribute) interactions_mutual_by_reference() (pypath.core.interaction.Interaction method) interactions_mutual_by_resource (pypath.core.network.Network attribute) interactions_mutual_by_resource() (pypath.core.interaction.Interaction method) interactions_negative_by_data_model (pypath.core.network.Network attribute) interactions_negative_by_data_model() (pypath.core.interaction.Interaction method) interactions_negative_by_interaction_type (pypath.core.network.Network attribute) interactions_negative_by_interaction_type() (pypath.core.interaction.Interaction method) interactions_negative_by_interaction_type_and_data_model (pypath.core.network.Network attribute) interactions_negative_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) interactions_negative_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) interactions_negative_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) interactions_negative_by_reference (pypath.core.network.Network attribute) interactions_negative_by_reference() (pypath.core.interaction.Interaction method) interactions_negative_by_resource (pypath.core.network.Network attribute) interactions_negative_by_resource() (pypath.core.interaction.Interaction method) interactions_non_directed_0_by_data_model (pypath.core.network.Network attribute) interactions_non_directed_0_by_data_model() (pypath.core.interaction.Interaction method) interactions_non_directed_0_by_interaction_type (pypath.core.network.Network attribute) interactions_non_directed_0_by_interaction_type() (pypath.core.interaction.Interaction method) interactions_non_directed_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute) interactions_non_directed_0_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) interactions_non_directed_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) interactions_non_directed_0_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) interactions_non_directed_0_by_reference (pypath.core.network.Network attribute) interactions_non_directed_0_by_reference() (pypath.core.interaction.Interaction method) interactions_non_directed_0_by_resource (pypath.core.network.Network attribute) interactions_non_directed_0_by_resource() (pypath.core.interaction.Interaction method) interactions_non_directed_by_data_model (pypath.core.network.Network attribute) interactions_non_directed_by_data_model() (pypath.core.interaction.Interaction method) interactions_non_directed_by_interaction_type (pypath.core.network.Network attribute) interactions_non_directed_by_interaction_type() (pypath.core.interaction.Interaction method) interactions_non_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute) interactions_non_directed_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) interactions_non_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) interactions_non_directed_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) interactions_non_directed_by_reference (pypath.core.network.Network attribute) interactions_non_directed_by_reference() (pypath.core.interaction.Interaction method) interactions_non_directed_by_resource (pypath.core.network.Network attribute) interactions_non_directed_by_resource() (pypath.core.interaction.Interaction method) interactions_positive_by_data_model (pypath.core.network.Network attribute) interactions_positive_by_data_model() (pypath.core.interaction.Interaction method) interactions_positive_by_interaction_type (pypath.core.network.Network attribute) interactions_positive_by_interaction_type() (pypath.core.interaction.Interaction method) interactions_positive_by_interaction_type_and_data_model (pypath.core.network.Network attribute) interactions_positive_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) interactions_positive_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) interactions_positive_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) interactions_positive_by_reference (pypath.core.network.Network attribute) interactions_positive_by_reference() (pypath.core.interaction.Interaction method) interactions_positive_by_resource (pypath.core.network.Network attribute) interactions_positive_by_resource() (pypath.core.interaction.Interaction method) interactions_signed_by_data_model (pypath.core.network.Network attribute) interactions_signed_by_data_model() (pypath.core.interaction.Interaction method) interactions_signed_by_interaction_type (pypath.core.network.Network attribute) interactions_signed_by_interaction_type() (pypath.core.interaction.Interaction method) interactions_signed_by_interaction_type_and_data_model (pypath.core.network.Network attribute) interactions_signed_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) interactions_signed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) interactions_signed_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) interactions_signed_by_reference (pypath.core.network.Network attribute) interactions_signed_by_reference() (pypath.core.interaction.Interaction method) interactions_signed_by_resource (pypath.core.network.Network attribute) interactions_signed_by_resource() (pypath.core.interaction.Interaction method) interactions_undirected_0_by_data_model (pypath.core.network.Network attribute) interactions_undirected_0_by_data_model() (pypath.core.interaction.Interaction method) interactions_undirected_0_by_interaction_type (pypath.core.network.Network attribute) interactions_undirected_0_by_interaction_type() (pypath.core.interaction.Interaction method) interactions_undirected_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute) interactions_undirected_0_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) interactions_undirected_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) interactions_undirected_0_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) interactions_undirected_0_by_reference (pypath.core.network.Network attribute) interactions_undirected_0_by_reference() (pypath.core.interaction.Interaction method) interactions_undirected_0_by_resource (pypath.core.network.Network attribute) interactions_undirected_0_by_resource() (pypath.core.interaction.Interaction method) interactions_undirected_by_data_model (pypath.core.network.Network attribute) interactions_undirected_by_data_model() (pypath.core.interaction.Interaction method) interactions_undirected_by_interaction_type (pypath.core.network.Network attribute) interactions_undirected_by_interaction_type() (pypath.core.interaction.Interaction method) interactions_undirected_by_interaction_type_and_data_model (pypath.core.network.Network attribute) interactions_undirected_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) interactions_undirected_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) interactions_undirected_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) interactions_undirected_by_reference (pypath.core.network.Network attribute) interactions_undirected_by_reference() (pypath.core.interaction.Interaction method) interactions_undirected_by_resource (pypath.core.network.Network attribute) interactions_undirected_by_resource() (pypath.core.interaction.Interaction method) IntercellAnnotation (class in pypath.core.intercell) Interface (class in pypath.internals.intera) InterPro (class in pypath.core.annot) interpro2go_annotations() (in module pypath.inputs.interpro) interpro_annotations() (in module pypath.inputs.interpro) interpro_entries() (in module pypath.inputs.interpro) interpro_xrefs() (in module pypath.inputs.interpro) Intersecting (class in pypath.utils.pyreact) InterSet (class in pypath.visual.drawing) Intogen (class in pypath.core.annot) intogen_annotations() (in module pypath.inputs.intogen) ipi_uniprot() (in module pypath.inputs.ipi) iptmnet_interactions() (in module pypath.inputs.iptmnet) IptmnetInteraction (class in pypath.inputs.iptmnet) is_directed() (pypath.core.interaction.Interaction method) is_directed_by_resources() (pypath.core.interaction.Interaction method) is_inhibition() (pypath.core.interaction.Interaction method) is_leaf() (pypath.utils.go.GeneOntology method) is_loop() (pypath.core.interaction.Interaction method) is_mutual() (pypath.core.interaction.Interaction method) is_mutual_by_resources() (pypath.core.interaction.Interaction method) is_name() (pypath.utils.go.GeneOntology method) is_not() (in module pypath.utils.reflists) (pypath.utils.reflists.ReferenceListManager method) is_quoted() (pypath.share.curl.Curl method) is_reviewed() (in module pypath.utils.uniprot) is_root() (pypath.utils.go.GeneOntology method) is_stimulation() (pypath.core.interaction.Interaction method) is_swissprot() (in module pypath.inputs.uniprot_db) is_term() (pypath.utils.go.GeneOntology method) is_trembl() (in module pypath.inputs.uniprot_db) is_uniprot() (in module pypath.inputs.uniprot_db) is_url() (in module pypath.share.curl) isdisjoint() (pypath.internals.annot_formats.AnnotationGroup class method) Italk (class in pypath.core.annot) italk_annotations() (in module pypath.inputs.italk) italk_interactions() (in module pypath.inputs.italk) italk_raw() (in module pypath.inputs.italk) items() (pypath.core.evidence.Evidences method) (pypath.internals.resource.NetworkDataset method) iter() (in module pypath.inputs.hmdb.common) (in module pypath.inputs.hmdb.metabolites) (in module pypath.inputs.hmdb.proteins) iter_evidences() (pypath.core.interaction.Interaction method) iter_match_evidences() (pypath.core.interaction.Interaction method) iterate() (pypath.utils.pyreact.BioPaxReader method) iterdb() (pypath.utils.seq.Pfam method) (pypath.utils.seq.Resource method) itermembers() (pypath.utils.pyreact.ComplexVariations method) iterprotein() (pypath.utils.seq.Pfam method) (pypath.utils.seq.Resource method) itertag() (in module pypath.utils.uniprot)

J

json_extract() (in module pypath.inputs.common)

json_read() (in module pypath.inputs.common)

K

kea_enzyme_substrate() (in module pypath.inputs.kea) kea_interactions() (in module pypath.inputs.kea) Kegg (class in pypath.core.complex) kegg (pypath.inputs.adrecs.AdrecsDrug attribute) kegg_dbget() (in module pypath.inputs.kegg) kegg_drug_to_chebi() (in module pypath.inputs.kegg_api) kegg_gene_to_ncbi_geneid() (in module pypath.inputs.kegg_api) kegg_gene_to_uniprot() (in module pypath.inputs.kegg_api) kegg_interactions() (in module pypath.inputs.kegg) kegg_medicus() (in module pypath.inputs.kegg) kegg_medicus_complexes() (in module pypath.inputs.kegg) kegg_medicus_interactions() (in module pypath.inputs.kegg) kegg_pathway_annotations() (in module pypath.inputs.kegg) kegg_pathway_annotations_pathwaycommons() (in module pypath.inputs.kegg) kegg_pathways (pypath.inputs.dorothea.DorotheaInteraction attribute) kegg_pathways() (in module pypath.inputs.kegg)

KeggPathway (class in pypath.inputs.kegg) KeggPathways (class in pypath.core.annot) KeggPathwaysPC (class in pypath.core.annot) key() (pypath.internals.intera.DomainMotif method) keys() (pypath.core.evidence.Evidences method) (pypath.internals.resource.NetworkDataset method) keywords (pypath.utils.uniprot.UniprotProtein property) keywords() (in module pypath.utils.uniprot) keywords_with_xrefs (pypath.utils.uniprot.UniprotProtein property) keywords_with_xrefs() (in module pypath.utils.uniprot) Kinasedotcom (class in pypath.core.annot) kinasedotcom_annotations() (in module pypath.inputs.kinasedotcom) Kirouac2010 (class in pypath.core.annot) kirouac2010_interactions() (in module pypath.inputs.kirouac2010) knowledge_filtered() (in module pypath.inputs.diseases) knowledge_full() (in module pypath.inputs.diseases)

L

label (pypath.core.network.NetworkStatsRecord attribute) (pypath.inputs.biogps.BiogpsDataset attribute) (pypath.internals.resource.NetworkResourceKey property) label() (in module pypath.utils.mapping) (pypath.utils.mapping.Mapper method) labels() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.CustomAnnotation method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) (pypath.core.intercell.IntercellAnnotation method) labels_by_data_model (pypath.core.network.Network attribute) labels_by_data_model() (pypath.core.interaction.Interaction method) labels_by_interaction_type (pypath.core.network.Network attribute) labels_by_interaction_type() (pypath.core.interaction.Interaction method) labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) labels_by_reference (pypath.core.network.Network attribute) labels_by_reference() (pypath.core.interaction.Interaction method) labels_by_resource (pypath.core.network.Network attribute) labels_by_resource() (pypath.core.interaction.Interaction method) Lambert2018 (class in pypath.core.annot) lambert2018_annotations() (in module pypath.inputs.lambert2018) lambert2018_s1_raw() (in module pypath.inputs.lambert2018) last (pypath.internals.resource.NetworkResourceKey property) latin (pypath.inputs.uniprot.Taxon attribute) latin_synonym (pypath.inputs.uniprot.Taxon attribute) laudanna_directions() (in module pypath.inputs.laudanna) laudanna_effects() (in module pypath.inputs.laudanna) length (pypath.utils.uniprot.UniprotProtein property) length() (in module pypath.utils.uniprot) lengths (pypath.utils.uniprot.UniprotProtein property) lengths() (in module pypath.utils.uniprot) level (pypath.inputs.dorothea.DorotheaInteraction attribute) level_to_int() (pypath.internals.license.LicenseAttrib class method) (pypath.internals.license.LicenseFeature class method) (pypath.internals.license.LicensePurpose class method) (pypath.internals.license.LicenseSharing class method) li2012_dmi() (in module pypath.inputs.li2012) li2012_enzyme_substrate() (in module pypath.inputs.li2012) li2012_interactions() (in module pypath.inputs.li2012) License (class in pypath.internals.license) license_filter() (pypath.resources.controller.ResourceController method) LicenseAttrib (class in pypath.internals.license) LicenseFeature (class in pypath.internals.license) LicensePurpose (class in pypath.internals.license) Licenses (class in pypath.resources.licenses) LicenseSharing (class in pypath.internals.license) ligand (pypath.inputs.cellinker.CellinkerInteraction attribute) (pypath.inputs.icellnet.IcellnetRecord attribute) ligand_location (pypath.inputs.cellinker.CellinkerInteraction attribute) LigandReceptor (class in pypath.core.annot) LightToDarkEdgeDrawer (class in pypath.visual.igraph_drawing.edge) limit (pypath.internals.annot_formats.AnnotDef attribute) lincs_compounds() (in module pypath.inputs.lincs) listof_ontologies() (in module pypath.inputs.ontology) lit_bm_13_interactions() (in module pypath.inputs.huri) lit_bm_17_interactions() (in module pypath.inputs.huri) lit_bm_interactions() (in module pypath.inputs.huri) lmpid_dmi() (in module pypath.inputs.lmpid) lmpid_interactions() (in module pypath.inputs.lmpid) lncdisease_interactions() (in module pypath.inputs.lncdisease) lncrna_identifiers_by_data_model (pypath.core.network.Network attribute) lncrna_identifiers_by_data_model() (pypath.core.interaction.Interaction method) lncrna_identifiers_by_interaction_type (pypath.core.network.Network attribute) lncrna_identifiers_by_interaction_type() (pypath.core.interaction.Interaction method) lncrna_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) lncrna_identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) lncrna_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) lncrna_identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) lncrna_identifiers_by_reference (pypath.core.network.Network attribute) lncrna_identifiers_by_reference() (pypath.core.interaction.Interaction method) lncrna_identifiers_by_resource (pypath.core.network.Network attribute) lncrna_identifiers_by_resource() (pypath.core.interaction.Interaction method) lncrna_labels_by_data_model (pypath.core.network.Network attribute) lncrna_labels_by_data_model() (pypath.core.interaction.Interaction method) lncrna_labels_by_interaction_type (pypath.core.network.Network attribute) lncrna_labels_by_interaction_type() (pypath.core.interaction.Interaction method) lncrna_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) lncrna_labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) lncrna_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) lncrna_labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) lncrna_labels_by_reference (pypath.core.network.Network attribute) lncrna_labels_by_reference() (pypath.core.interaction.Interaction method) lncrna_labels_by_resource (pypath.core.network.Network attribute) lncrna_labels_by_resource() (pypath.core.interaction.Interaction method) lncrnadb_interactions() (in module pypath.inputs.lncrnadb) lncrnas_by_data_model (pypath.core.network.Network attribute) lncrnas_by_data_model() (pypath.core.interaction.Interaction method) lncrnas_by_interaction_type (pypath.core.network.Network attribute) lncrnas_by_interaction_type() (pypath.core.interaction.Interaction method) lncrnas_by_interaction_type_and_data_model (pypath.core.network.Network attribute) lncrnas_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) lncrnas_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) lncrnas_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) lncrnas_by_reference (pypath.core.network.Network attribute) lncrnas_by_reference() (pypath.core.interaction.Interaction method) lncrnas_by_resource (pypath.core.network.Network attribute) lncrnas_by_resource() (pypath.core.interaction.Interaction method) load() (in module pypath.utils.uniprot) (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) (pypath.core.network.Network method) (pypath.utils.mapping.MapReader method) (pypath.utils.orthology.HomologeneOrthology method) (pypath.utils.seq.Pfam method) (pypath.utils.seq.Resource method)

load_data() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) (pypath.core.complex.AbstractComplexResource method) (pypath.core.complex.Cellchatdb method) (pypath.core.complex.Cellinker method) (pypath.core.complex.CellPhoneDB method) (pypath.core.complex.Compleat method) (pypath.core.complex.ComplexAggregator method) (pypath.core.complex.ComplexPortal method) (pypath.core.complex.Corum method) (pypath.core.complex.GuideToPharmacology method) (pypath.core.complex.Havugimana method) (pypath.core.complex.Hpmr method) (pypath.core.complex.Humap method) (pypath.core.complex.Humap2 method) (pypath.core.complex.Icellnet method) (pypath.core.complex.Kegg method) (pypath.core.complex.Pdb method) (pypath.core.complex.Signor method) (pypath.core.complex.Spike method) (pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method) (pypath.core.enz_sub.EnzymeSubstrateProcessor method) (pypath.internals.resource.AbstractResource method) load_dataset() (pypath.omnipath.app.DatabaseManager method) load_from_pickle() (pypath.core.network.Network method) load_genesymbol5() (pypath.utils.mapping.Mapper method) load_go() (in module pypath.utils.go) load_lmpid() (in module pypath.inputs.lmpid) load_mapping() (pypath.utils.mapping.Mapper method) (pypath.utils.pdb.ResidueMapper method) load_proteins() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) load_resource() (pypath.core.network.Network method) load_resources() (pypath.core.network.Network method) load_uniprot_static() (pypath.utils.mapping.Mapper method) Locate (class in pypath.core.annot) locate_localizations() (in module pypath.inputs.locate) log() (in module pypath) lowest() (pypath.utils.go.GeneOntology method) Lrdb (class in pypath.core.annot) lrdb_annotations() (in module pypath.inputs.lrdb) lrdb_interactions() (in module pypath.inputs.lrdb) LrdbAnnotation (class in pypath.inputs.lrdb)

M

macrophage_interactions() (in module pypath.inputs.macrophage) majority_dir() (pypath.core.interaction.Interaction method) majority_sign() (pypath.core.interaction.Interaction method) make_df() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.CustomAnnotation method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) (pypath.core.intercell.IntercellAnnotation method) (pypath.core.network.Network method) (pypath.omnipath.export.Export method) map_name() (in module pypath.utils.mapping) (pypath.utils.mapping.Mapper method) map_name0() (in module pypath.utils.mapping) (pypath.utils.mapping.Mapper method) map_names() (in module pypath.utils.mapping) (pypath.utils.mapping.Mapper method) Mapper (class in pypath.utils.mapping) mapping() (in module pypath.inputs.hmdb.common) (in module pypath.inputs.hmdb.metabolites) (in module pypath.inputs.hmdb.proteins) mapping_table_a_to_b (pypath.utils.mapping.MapReader property) mapping_table_b_to_a (pypath.utils.mapping.MapReader property) mapping_tables() (in module pypath.utils.mapping) (pypath.utils.mapping.Mapper static method) MappingInput (class in pypath.internals.input_formats) MappingTable (class in pypath.utils.mapping) MappingTableKey (class in pypath.utils.mapping) MapReader (class in pypath.utils.mapping) match() (pypath.utils.orthology.EnsemblOrthology method) (pypath.utils.orthology.OmaOrthology method) Matrisome (class in pypath.core.annot) matrisome_annotations() (in module pypath.inputs.matrisome) Matrixdb (class in pypath.core.annot) matrixdb_annotations() (in module pypath.inputs.matrixdb) matrixdb_ecm_proteins() (in module pypath.inputs.matrixdb) matrixdb_interactions() (in module pypath.inputs.matrixdb) matrixdb_membrane_proteins() (in module pypath.inputs.matrixdb) matrixdb_secreted_proteins() (in module pypath.inputs.matrixdb) Mcam (class in pypath.core.annot) mcam_cell_adhesion_molecules() (in module pypath.inputs.mcam) meddra (pypath.inputs.adrecs.AdrecsTerm attribute) meddra_id (pypath.inputs.sider.SiderSideeffectMeddra attribute) Membranome (class in pypath.core.annot) membranome_annotations() (in module pypath.inputs.membranome) merge() (pypath.core.evidence.Evidence method) (pypath.core.interaction.Interaction method) (pypath.internals.intera.Complex method) merge_complexes() (pypath.utils.pyreact.PyReact method) merge_cvariations() (pypath.utils.pyreact.PyReact method) mesh (pypath.inputs.adrecs.AdrecsDrug attribute) method (pypath.core.network.NetworkStatsRecord attribute) microbe_ncbi_tax_id (pypath.inputs.gutmgene.GutmgeneAnnotation attribute) (pypath.inputs.gutmgene.GutmgeneRaw attribute) microbe_taxon (pypath.inputs.gutmgene.GutmgeneAnnotation attribute) (pypath.inputs.gutmgene.GutmgeneRaw attribute) mimp_enzyme_substrate() (in module pypath.inputs.mimp) mimp_interactions() (in module pypath.inputs.mimp) mir2disease_interactions() (in module pypath.inputs.mir2disease) mirbase_ids() (in module pypath.inputs.mirbase) mirbase_mature() (in module pypath.inputs.mirbase) mirbase_mature_all() (in module pypath.inputs.mirbase) mirbase_precursor() (in module pypath.inputs.mirbase) mirbase_precursor_all() (in module pypath.inputs.mirbase) mirbase_precursor_to_mature() (in module pypath.inputs.mirbase) mirdeathdb_interactions() (in module pypath.inputs.mirdeathdb) mirecords_interactions() (in module pypath.inputs.mirecords) mirna_identifiers_by_data_model (pypath.core.network.Network attribute) mirna_identifiers_by_data_model() (pypath.core.interaction.Interaction method) mirna_identifiers_by_interaction_type (pypath.core.network.Network attribute) mirna_identifiers_by_interaction_type() (pypath.core.interaction.Interaction method) mirna_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) mirna_identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) mirna_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) mirna_identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) mirna_identifiers_by_reference (pypath.core.network.Network attribute) mirna_identifiers_by_reference() (pypath.core.interaction.Interaction method) mirna_identifiers_by_resource (pypath.core.network.Network attribute) mirna_identifiers_by_resource() (pypath.core.interaction.Interaction method) mirna_labels_by_data_model (pypath.core.network.Network attribute) mirna_labels_by_data_model() (pypath.core.interaction.Interaction method) mirna_labels_by_interaction_type (pypath.core.network.Network attribute) mirna_labels_by_interaction_type() (pypath.core.interaction.Interaction method) mirna_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) mirna_labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) mirna_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) mirna_labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) mirna_labels_by_reference (pypath.core.network.Network attribute) mirna_labels_by_reference() (pypath.core.interaction.Interaction method) mirna_labels_by_resource (pypath.core.network.Network attribute) mirna_labels_by_resource() (pypath.core.interaction.Interaction method) mirna_target() (pypath.core.network.Network class method) mirnas_by_data_model (pypath.core.network.Network attribute) mirnas_by_data_model() (pypath.core.interaction.Interaction method) mirnas_by_interaction_type (pypath.core.network.Network attribute) mirnas_by_interaction_type() (pypath.core.interaction.Interaction method) mirnas_by_interaction_type_and_data_model (pypath.core.network.Network attribute) mirnas_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) mirnas_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) mirnas_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) mirnas_by_reference (pypath.core.network.Network attribute) mirnas_by_reference() (pypath.core.interaction.Interaction method) mirnas_by_resource (pypath.core.network.Network attribute) mirnas_by_resource() (pypath.core.interaction.Interaction method) mirtarbase_interactions() (in module pypath.inputs.mirtarbase) mitab_field_list() (in module pypath.inputs.mitab) mitab_field_uniprot() (in module pypath.inputs.mitab) module pypath pypath.core pypath.core.annot pypath.core.attrs pypath.core.common pypath.core.complex pypath.core.entity pypath.core.enz_sub pypath.core.evidence pypath.core.interaction pypath.core.intercell pypath.core.intercell_annot pypath.core.network pypath.data pypath.inputs pypath.inputs.abs pypath.inputs.acsn pypath.inputs.adhesome pypath.inputs.adrecs pypath.inputs.almen2009 pypath.inputs.baccin2019 pypath.inputs.biogps pypath.inputs.biogrid pypath.inputs.biomart pypath.inputs.biomodels pypath.inputs.ca1 pypath.inputs.cancercellmap pypath.inputs.cancerdrugsdb pypath.inputs.cancersea pypath.inputs.cell pypath.inputs.cellcall pypath.inputs.cellcellinteractions pypath.inputs.cellchatdb pypath.inputs.cellinker pypath.inputs.cellphonedb pypath.inputs.celltalkdb pypath.inputs.celltypist pypath.inputs.chembl pypath.inputs.clinvar pypath.inputs.collectri pypath.inputs.common pypath.inputs.compath pypath.inputs.compleat pypath.inputs.complexportal pypath.inputs.comppi pypath.inputs.connectomedb pypath.inputs.corum pypath.inputs.cosmic pypath.inputs.cpad pypath.inputs.cpdb pypath.inputs.credentials pypath.inputs.csa pypath.inputs.cspa pypath.inputs.ctdbase pypath.inputs.cytosig pypath.inputs.dbptm pypath.inputs.ddinter pypath.inputs.deathdomain pypath.inputs.depod pypath.inputs.dgidb pypath.inputs.dip pypath.inputs.diseases pypath.inputs.domino pypath.inputs.dorothea pypath.inputs.drugbank pypath.inputs.drugcentral pypath.inputs.ebi pypath.inputs.elm pypath.inputs.embopress pypath.inputs.embrace pypath.inputs.encode pypath.inputs.ensembl pypath.inputs.eutils pypath.inputs.exocarta pypath.inputs.expasy pypath.inputs.genecards pypath.inputs.go pypath.inputs.gpcrdb pypath.inputs.graphviz pypath.inputs.guide2pharma pypath.inputs.gutmgene pypath.inputs.havugimana pypath.inputs.hgnc pypath.inputs.hippie pypath.inputs.hmdb pypath.inputs.hmdb.common pypath.inputs.hmdb.metabolites pypath.inputs.hmdb.proteins pypath.inputs.hmdb.schema pypath.inputs.hmdb.schema.common pypath.inputs.hmdb.schema.metabolites pypath.inputs.hmdb.schema.proteins pypath.inputs.hmdb.structures pypath.inputs.hmdb.visual pypath.inputs.hmdb.xml pypath.inputs.homologene pypath.inputs.hpmr pypath.inputs.hpo pypath.inputs.hprd pypath.inputs.htri pypath.inputs.humancellmap pypath.inputs.humap pypath.inputs.humsavar pypath.inputs.huri pypath.inputs.i3d pypath.inputs.icellnet pypath.inputs.ielm pypath.inputs.imweb pypath.inputs.innatedb pypath.inputs.instruct pypath.inputs.intact pypath.inputs.integrins pypath.inputs.interpro pypath.inputs.intogen pypath.inputs.ipi pypath.inputs.iptmnet pypath.inputs.italk pypath.inputs.kea pypath.inputs.kegg pypath.inputs.kegg_api pypath.inputs.kinasedotcom pypath.inputs.kirouac2010 pypath.inputs.lambert2018 pypath.inputs.laudanna pypath.inputs.li2012 pypath.inputs.lincs pypath.inputs.lipidmaps pypath.inputs.lipidmaps.structures pypath.inputs.lmpid pypath.inputs.lncdisease pypath.inputs.lncrnadb pypath.inputs.locate pypath.inputs.lrdb pypath.inputs.macrophage pypath.inputs.main pypath.inputs.matrisome pypath.inputs.matrixdb pypath.inputs.mcam pypath.inputs.membranome pypath.inputs.mimp pypath.inputs.mir2disease pypath.inputs.mirbase pypath.inputs.mirdeathdb pypath.inputs.mirecords pypath.inputs.mirtarbase pypath.inputs.mitab pypath.inputs.mppi pypath.inputs.msigdb pypath.inputs.ncrdeathdb pypath.inputs.negatome pypath.inputs.netbiol pypath.inputs.netpath pypath.inputs.offsides pypath.inputs.oma pypath.inputs.ontology pypath.inputs.opentargets pypath.inputs.opm pypath.inputs.oreganno pypath.inputs.panglaodb pypath.inputs.pathophenodb pypath.inputs.pathwaycommons pypath.inputs.pazar pypath.inputs.pdb pypath.inputs.pdzbase pypath.inputs.pepcyber pypath.inputs.pfam pypath.inputs.pharos pypath.inputs.phobius pypath.inputs.phosphatome pypath.inputs.phosphoelm pypath.inputs.phosphonetworks pypath.inputs.phosphopoint pypath.inputs.phosphosite pypath.inputs.pisa pypath.inputs.pro pypath.inputs.progeny pypath.inputs.proteinatlas pypath.inputs.proteins pypath.inputs.protmapper pypath.inputs.pubchem pypath.inputs.pubmed pypath.inputs.ramilowski2015 pypath.inputs.ramp pypath.inputs.rdata pypath.inputs.reaction pypath.inputs.reactome pypath.inputs.scconnect pypath.inputs.science pypath.inputs.sider pypath.inputs.signalink pypath.inputs.signor pypath.inputs.spike pypath.inputs.stitch pypath.inputs.string pypath.inputs.surfaceome pypath.inputs.swisslipids pypath.inputs.switches_elm pypath.inputs.talklr pypath.inputs.tcdb pypath.inputs.tfcensus pypath.inputs.threedcomplex pypath.inputs.threedid pypath.inputs.topdb pypath.inputs.transmir pypath.inputs.trip pypath.inputs.trrust pypath.inputs.twosides pypath.inputs.unichem pypath.inputs.uniprot pypath.inputs.uniprot_db pypath.inputs.uniprot_idmapping pypath.inputs.wang pypath.inputs.wojtowicz2020 pypath.inputs.zhong2015 pypath.internals pypath.internals.annot_formats pypath.internals.input_formats pypath.internals.intera pypath.internals.license pypath.internals.maps pypath.internals.refs pypath.internals.resource pypath.legacy pypath.legacy.db_categories pypath.omnipath pypath.omnipath.app pypath.omnipath.databases pypath.omnipath.databases.define pypath.omnipath.export pypath.omnipath.param pypath.omnipath.server pypath.omnipath.server.build pypath.omnipath.server.generate_about_page pypath.omnipath.server.legacy pypath.omnipath.server.run pypath.resources pypath.resources.controller pypath.resources.data pypath.resources.data_formats pypath.resources.descriptions pypath.resources.licenses pypath.resources.network pypath.resources.urls pypath.share pypath.share.cache pypath.share.common pypath.share.constants pypath.share.curl pypath.share.progress pypath.share.session pypath.share.settings pypath.utils pypath.utils.go pypath.utils.mapping pypath.utils.metabo pypath.utils.orthology pypath.utils.pdb pypath.utils.proteomicsdb pypath.utils.pyreact pypath.utils.reflists pypath.utils.residues pypath.utils.seq pypath.utils.taxonomy pypath.utils.unichem pypath.utils.uniprot pypath.visual pypath.visual.drawing pypath.visual.igraph_drawing pypath.visual.igraph_drawing.edge pypath.visual.igraph_drawing.vertex

Motif (class in pypath.internals.intera) mppi_interactions() (in module pypath.inputs.mppi) mro() (pypath.utils.orthology.OrthologMeta method) Msigdb (class in pypath.core.annot) msigdb_annotations() (in module pypath.inputs.msigdb) msigdb_download() (in module pypath.inputs.msigdb) msigdb_download_collections() (in module pypath.inputs.msigdb)

N

name (pypath.inputs.adrecs.AdrecsTerm attribute) (pypath.inputs.pathwaycommons.PathwayCommonsResource attribute) (pypath.inputs.sider.SiderDrug attribute) (pypath.internals.annot_formats.AnnotDef attribute) (pypath.internals.annot_formats.AnnotDefKey attribute) (pypath.internals.resource.EnzymeSubstrateResourceKey attribute) (pypath.internals.resource.NetworkResourceKey attribute) name_process (pypath.inputs.uniprot.UniprotQuery attribute) names_to_terms() (pypath.utils.go.GeneOntology method) names_to_terms_aspects() (pypath.utils.go.GeneOntology method) ncbi_id (pypath.inputs.uniprot.Taxon attribute) ncbi_tax_id (pypath.utils.mapping.MappingTableKey attribute) ncrdeathdb_interactions() (in module pypath.inputs.ncrdeathdb) negative_a_b() (pypath.core.interaction.Interaction method) negative_b_a() (pypath.core.interaction.Interaction method) negative_resources_a_b() (pypath.core.interaction.Interaction method) negative_resources_b_a() (pypath.core.interaction.Interaction method) negative_reverse() (pypath.core.interaction.Interaction method) negative_straight() (pypath.core.interaction.Interaction method) negatome_interactions() (in module pypath.inputs.negatome) netpath_interactions() (in module pypath.inputs.netpath) netpath_names() (in module pypath.inputs.netpath) netpath_pathway_annotations() (in module pypath.inputs.netpath) NetpathPathways (class in pypath.core.annot) Network (class in pypath.core.network) network_df() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) (pypath.omnipath.app.DatabaseManager method) network_df_by_source() (pypath.omnipath.app.DatabaseManager method) NetworkDataset (class in pypath.internals.resource) NetworkEntityCollection (class in pypath.core.network) NetworkInput (class in pypath.internals.input_formats) NetworkResource (class in pypath.internals.resource) NetworkResourceKey (class in pypath.internals.resource) NetworkStatsRecord (class in pypath.core.network) nrf2ome_interactions() (in module pypath.inputs.netbiol) number (pypath.inputs.uniprot.UniprotRecordHistory attribute) numof_entities() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) numof_interactions_per_reference() (pypath.core.network.Network method) numof_records() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method)

numof_references() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) numof_residues() (pypath.internals.intera.Interface method)

O

offset (pypath.utils.pdb.Residue attribute) offsides_side_effects() (in module pypath.inputs.offsides) oma_orthologs() (in module pypath.inputs.oma) oma_table() (in module pypath.inputs.oma) OmaOrtholog (class in pypath.utils.orthology) OmaOrthology (class in pypath.utils.orthology) only_pmids() (in module pypath.inputs.pubmed) only_swissprot (pypath.utils.orthology.OrthologyTableKey attribute) only_uniprot_ac() (pypath.utils.mapping.Mapper method) ontology() (in module pypath.inputs.ontology) op (pypath.internals.annot_formats.AnnotOp attribute) open() (pypath.share.curl.Curl method) (pypath.share.curl.FileOpener method) open_biopax() (pypath.utils.pyreact.BioPaxReader method) open_pubmed() (in module pypath.inputs.pubmed) open_tgz() (pypath.share.curl.Curl method) (pypath.share.curl.FileOpener method)

opentargets_adverse_reactions() (in module pypath.inputs.opentargets) opentargets_baseline_expression() (in module pypath.inputs.opentargets) opentargets_direct_score() (in module pypath.inputs.opentargets) opentargets_general() (in module pypath.inputs.opentargets) opentargets_indirect_score() (in module pypath.inputs.opentargets) Opm (class in pypath.core.annot) opm_annotations() (in module pypath.inputs.opm) oreganno_interactions() (in module pypath.inputs.oreganno) oreganno_raw() (in module pypath.inputs.oreganno) organism (pypath.inputs.biogps.BiogpsDataset attribute) organism() (in module pypath.utils.uniprot) organisms_check() (pypath.core.network.Network method) OrthologBase (class in pypath.utils.orthology) OrthologMeta (class in pypath.utils.orthology) OrthologyManager (class in pypath.utils.orthology) OrthologyTableKey (class in pypath.utils.orthology) other_organism_uniprot() (pypath.utils.mapping.Mapper method)

P

pandas_matrix() (pypath.utils.proteomicsdb.ProteomicsDB method) Panglaodb (class in pypath.core.annot) panglaodb_annotations() (in module pypath.inputs.panglaodb) panglaodb_raw() (in module pypath.inputs.panglaodb) panther_biopax() (in module pypath.inputs.reaction) panther_interactions() (in module pypath.inputs.reaction) parent (pypath.inputs.adrecs.AdrecsChildParent attribute) (pypath.internals.annot_formats.AnnotDef attribute) (pypath.internals.annot_formats.AnnotDefKey attribute) partner (pypath.inputs.hpmr.HpmrInteraction attribute) partner_role (pypath.inputs.hpmr.HpmrInteraction attribute) partners() (pypath.core.network.Network method) pathogen (pypath.inputs.pathophenodb.DiseasePathogen attribute) pathogen_taxid (pypath.inputs.pathophenodb.DiseasePathogen attribute) pathway (pypath.inputs.kegg.KeggPathway attribute) pathway_bad (in module pypath.resources.data_formats) pathway_to_disease() (in module pypath.inputs.kegg_api) pathway_to_drug() (in module pypath.inputs.kegg_api) pathway_to_gene() (in module pypath.inputs.kegg_api) pathwaycommons_bind_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_biogrid_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_corum_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_dip_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_hprd_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_inoh_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_intact_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_kegg_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_netpath_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_panther_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_phosphosite_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_reactome_interactions() (in module pypath.inputs.pathwaycommons) pathwaycommons_wikipathways_interactions() (in module pypath.inputs.pathwaycommons) PathwayCommonsInteraction (class in pypath.inputs.pathwaycommons) PathwayCommonsResource (class in pypath.inputs.pathwaycommons) pazar_interactions() (in module pypath.inputs.pazar) pc_label (pypath.inputs.pathwaycommons.PathwayCommonsResource attribute) Pdb (class in pypath.core.complex) pdb_chains() (in module pypath.inputs.pdb) pdb_complexes() (in module pypath.inputs.pdb) pdb_end (pypath.utils.pdb.Segment attribute) pdb_start (pypath.utils.pdb.Segment attribute) pdb_uniprot() (in module pypath.inputs.pdb) pdzbase_interactions() (in module pypath.inputs.pdzbase) pepcyber_details() (in module pypath.inputs.pepcyber) pepcyber_interactions() (in module pypath.inputs.pepcyber) percent (pypath.core.network.NetworkStatsRecord attribute) percent_cat (pypath.core.network.NetworkStatsRecord attribute) percent_res_cat (pypath.core.network.NetworkStatsRecord attribute) perform() (pypath.inputs.uniprot.UniprotQuery method) peripheral (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute) Pfam (class in pypath.utils.seq) pfam_names() (in module pypath.inputs.pfam) pfam_pdb() (in module pypath.inputs.pfam) pfam_regions() (in module pypath.inputs.pfam) pfam_uniprot() (in module pypath.inputs.pfam) pharos_diseases() (in module pypath.inputs.pharos) pharos_expression() (in module pypath.inputs.pharos) pharos_general() (in module pypath.inputs.pharos) pharos_gtex() (in module pypath.inputs.pharos) pharos_ligands() (in module pypath.inputs.pharos) pharos_orthologs() (in module pypath.inputs.pharos) pharos_targets() (in module pypath.inputs.pharos) pharos_xrefs() (in module pypath.inputs.pharos) Phobius (class in pypath.core.annot) phobius_annotations() (in module pypath.inputs.phobius) Phosphatome (class in pypath.core.annot) phosphatome_annotations() (in module pypath.inputs.phosphatome) phosphoelm_enzyme_substrate() (in module pypath.inputs.phosphoelm) phosphoelm_interactions() (in module pypath.inputs.phosphoelm) phosphoelm_kinases() (in module pypath.inputs.phosphoelm) phosphonetworks_enzyme_substrate() (in module pypath.inputs.phosphonetworks) phosphonetworks_interactions() (in module pypath.inputs.phosphonetworks) phosphopoint_directions() (in module pypath.inputs.phosphopoint) phosphopoint_interactions() (in module pypath.inputs.phosphopoint) phosphosite_directions() (in module pypath.inputs.phosphosite) phosphosite_enzyme_substrate() (in module pypath.inputs.phosphosite) phosphosite_interactions() (in module pypath.inputs.phosphosite) phosphosite_interactions_all() (in module pypath.inputs.phosphosite) phosphosite_interactions_curated() (in module pypath.inputs.phosphosite) phosphosite_interactions_new() (in module pypath.inputs.phosphosite) phosphosite_interactions_noref() (in module pypath.inputs.phosphosite) phosphosite_ptm_orthology() (in module pypath.inputs.phosphosite) phosphosite_ptms() (in module pypath.inputs.phosphosite) phosphosite_regsites() (in module pypath.inputs.phosphosite) phosphosite_regsites_one_organism() (in module pypath.inputs.phosphosite) pickle_exists() (pypath.omnipath.app.DatabaseManager method) pickle_path() (pypath.omnipath.app.DatabaseManager method) PickleMapping (class in pypath.internals.input_formats) pid_biopax() (in module pypath.inputs.reaction) pid_interactions() (in module pypath.inputs.reaction) pisa_bonds() (in module pypath.inputs.pisa) pisa_interfaces() (in module pypath.inputs.pisa) PisaBond (class in pypath.inputs.pisa) Plot (class in pypath.visual.drawing) pmids (pypath.inputs.cellinker.CellinkerInteraction attribute) pmids_dict() (in module pypath.inputs.pubmed) pmids_list() (in module pypath.inputs.pubmed) pop() (pypath.internals.resource.NetworkDataset method) popitem() (pypath.internals.resource.NetworkDataset method) populate_classes() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) populate_scores() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) positive_a_b() (pypath.core.interaction.Interaction method) positive_b_a() (pypath.core.interaction.Interaction method) positive_resources_a_b() (pypath.core.interaction.Interaction method) positive_resources_b_a() (pypath.core.interaction.Interaction method) positive_reverse() (pypath.core.interaction.Interaction method) positive_straight() (pypath.core.interaction.Interaction method) post_transcriptionally_activated_by (pypath.core.network.Network attribute) post_transcriptionally_activates (pypath.core.network.Network attribute) post_transcriptionally_regulated_by (pypath.core.network.Network attribute) post_transcriptionally_regulates (pypath.core.network.Network attribute) post_transcriptionally_suppressed_by (pypath.core.network.Network attribute) post_transcriptionally_suppresses (pypath.core.network.Network attribute) post_translationally_activated_by (pypath.core.network.Network attribute) post_translationally_activates (pypath.core.network.Network attribute) post_translationally_regulated_by (pypath.core.network.Network attribute) post_translationally_regulates (pypath.core.network.Network attribute) post_translationally_suppressed_by (pypath.core.network.Network attribute) post_translationally_suppresses (pypath.core.network.Network attribute) predicted (pypath.inputs.dorothea.DorotheaInteraction attribute) predicted_sources (pypath.inputs.dorothea.DorotheaInteraction attribute) preserve_off (class in pypath.share.curl) preserve_on (class in pypath.share.curl) primary_uniprot() (pypath.utils.mapping.Mapper method) print_features() (in module pypath.utils.uniprot) pro_mapping() (in module pypath.inputs.pro) process() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) (pypath.core.complex.AbstractComplexResource method) (pypath.core.complex.Cellchatdb method) (pypath.core.complex.Cellinker method) (pypath.core.complex.CellPhoneDB method) (pypath.core.complex.Compleat method) (pypath.core.complex.ComplexAggregator method) (pypath.core.complex.ComplexPortal method) (pypath.core.complex.Corum method) (pypath.core.complex.GuideToPharmacology method) (pypath.core.complex.Havugimana method) (pypath.core.complex.Hpmr method) (pypath.core.complex.Humap method) (pypath.core.complex.Humap2 method) (pypath.core.complex.Icellnet method) (pypath.core.complex.Kegg method) (pypath.core.complex.Pdb method) (pypath.core.complex.Signor method) (pypath.core.complex.Spike method) (pypath.internals.resource.AbstractResource method) (pypath.utils.pyreact.BioPaxReader method) process_3did_dmi() (in module pypath.inputs.threedid) process_annot() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) process_categories() (pypath.core.annot.GOCustomIntercell method) (pypath.utils.go.GOCustomAnnotation method) process_complex() (in module pypath.inputs.reaction) process_controls() (in module pypath.inputs.reaction) process_reactions() (in module pypath.inputs.reaction) processed() (in module pypath.inputs.hmdb.common) (in module pypath.inputs.hmdb.metabolites) processor() (pypath.utils.seq.Pfam method) (pypath.utils.seq.Resource method) Progeny (class in pypath.core.annot) progeny_annotations() (in module pypath.inputs.progeny) progeny_raw() (in module pypath.inputs.progeny) Progress (class in pypath.share.progress) ProMapping (class in pypath.internals.input_formats) Protein (class in pypath.utils.pyreact) protein_datasheet() (in module pypath.inputs.uniprot) protein_identifiers_by_data_model (pypath.core.network.Network attribute) protein_identifiers_by_data_model() (pypath.core.interaction.Interaction method) protein_identifiers_by_interaction_type (pypath.core.network.Network attribute) protein_identifiers_by_interaction_type() (pypath.core.interaction.Interaction method) protein_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) protein_identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) protein_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) protein_identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) protein_identifiers_by_reference (pypath.core.network.Network attribute) protein_identifiers_by_reference() (pypath.core.interaction.Interaction method) protein_identifiers_by_resource (pypath.core.network.Network attribute) protein_identifiers_by_resource() (pypath.core.interaction.Interaction method) protein_labels_by_data_model (pypath.core.network.Network attribute) protein_labels_by_data_model() (pypath.core.interaction.Interaction method) protein_labels_by_interaction_type (pypath.core.network.Network attribute) protein_labels_by_interaction_type() (pypath.core.interaction.Interaction method) protein_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) protein_labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) protein_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) protein_labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) protein_labels_by_reference (pypath.core.network.Network attribute) protein_labels_by_reference() (pypath.core.interaction.Interaction method) protein_labels_by_resource (pypath.core.network.Network attribute) protein_labels_by_resource() (pypath.core.interaction.Interaction method) proteinatlas_annotations() (in module pypath.inputs.proteinatlas) proteinatlas_secretome_annotations() (in module pypath.inputs.proteinatlas) proteinatlas_subcellular_annotations() (in module pypath.inputs.proteinatlas) ProteinFamily (class in pypath.utils.pyreact) ProteinOrthology (class in pypath.utils.orthology) proteins_by_data_model (pypath.core.network.Network attribute) proteins_by_data_model() (pypath.core.interaction.Interaction method) proteins_by_interaction_type (pypath.core.network.Network attribute) proteins_by_interaction_type() (pypath.core.interaction.Interaction method) proteins_by_interaction_type_and_data_model (pypath.core.network.Network attribute) proteins_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) proteins_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) proteins_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) proteins_by_reference (pypath.core.network.Network attribute) proteins_by_reference() (pypath.core.interaction.Interaction method) proteins_by_resource (pypath.core.network.Network attribute) proteins_by_resource() (pypath.core.interaction.Interaction method) Proteomes (class in pypath.utils.orthology) ProteomicsDB (class in pypath.utils.proteomicsdb) protmapper_enzyme_substrate() (in module pypath.inputs.protmapper) protmapper_interactions() (in module pypath.inputs.protmapper) Ptm (class in pypath.internals.intera) ptm() (in module pypath.utils.uniprot) ptm_orthology() (pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method) (pypath.utils.orthology.PtmOrthology method) ptm_type (pypath.inputs.iptmnet.IptmnetInteraction attribute) ptm_with_xrefs() (in module pypath.utils.uniprot) PtmOrthology (class in pypath.utils.orthology) pubchem_cid (pypath.inputs.adrecs.AdrecsDrug attribute) pubchem_mapping() (in module pypath.inputs.pubchem) pubmed (pypath.inputs.dorothea.DorotheaInteraction attribute) pubmeds (pypath.core.evidence.Evidence property) pypath module pypath.core module pypath.core.annot module pypath.core.attrs module pypath.core.common module pypath.core.complex module pypath.core.entity module pypath.core.enz_sub module pypath.core.evidence module pypath.core.interaction module pypath.core.intercell module pypath.core.intercell_annot module pypath.core.network module pypath.data module pypath.inputs module pypath.inputs.abs module pypath.inputs.acsn module pypath.inputs.adhesome module pypath.inputs.adrecs module pypath.inputs.almen2009 module pypath.inputs.baccin2019 module pypath.inputs.biogps module pypath.inputs.biogrid module pypath.inputs.biomart module pypath.inputs.biomodels module pypath.inputs.ca1 module pypath.inputs.cancercellmap module pypath.inputs.cancerdrugsdb module pypath.inputs.cancersea module pypath.inputs.cell module pypath.inputs.cellcall module pypath.inputs.cellcellinteractions module pypath.inputs.cellchatdb module pypath.inputs.cellinker module pypath.inputs.cellphonedb module pypath.inputs.celltalkdb module pypath.inputs.celltypist module pypath.inputs.chembl module pypath.inputs.clinvar module pypath.inputs.collectri module pypath.inputs.common module pypath.inputs.compath module pypath.inputs.compleat module pypath.inputs.complexportal module pypath.inputs.comppi module pypath.inputs.connectomedb module pypath.inputs.corum module pypath.inputs.cosmic module pypath.inputs.cpad module pypath.inputs.cpdb module pypath.inputs.credentials module pypath.inputs.csa module pypath.inputs.cspa module pypath.inputs.ctdbase module pypath.inputs.cytosig module pypath.inputs.dbptm module pypath.inputs.ddinter module pypath.inputs.deathdomain module

pypath.inputs.depod module pypath.inputs.dgidb module pypath.inputs.dip module pypath.inputs.diseases module pypath.inputs.domino module pypath.inputs.dorothea module pypath.inputs.drugbank module pypath.inputs.drugcentral module pypath.inputs.ebi module pypath.inputs.elm module pypath.inputs.embopress module pypath.inputs.embrace module pypath.inputs.encode module pypath.inputs.ensembl module pypath.inputs.eutils module pypath.inputs.exocarta module pypath.inputs.expasy module pypath.inputs.genecards module pypath.inputs.go module pypath.inputs.gpcrdb module pypath.inputs.graphviz module pypath.inputs.guide2pharma module pypath.inputs.gutmgene module pypath.inputs.havugimana module pypath.inputs.hgnc module pypath.inputs.hippie module pypath.inputs.hmdb module pypath.inputs.hmdb.common module pypath.inputs.hmdb.metabolites module pypath.inputs.hmdb.proteins module pypath.inputs.hmdb.schema module pypath.inputs.hmdb.schema.common module pypath.inputs.hmdb.schema.metabolites module pypath.inputs.hmdb.schema.proteins module pypath.inputs.hmdb.structures module pypath.inputs.hmdb.visual module pypath.inputs.hmdb.xml module pypath.inputs.homologene module pypath.inputs.hpmr module pypath.inputs.hpo module pypath.inputs.hprd module pypath.inputs.htri module pypath.inputs.humancellmap module pypath.inputs.humap module pypath.inputs.humsavar module pypath.inputs.huri module pypath.inputs.i3d module pypath.inputs.icellnet module pypath.inputs.ielm module pypath.inputs.imweb module pypath.inputs.innatedb module pypath.inputs.instruct module pypath.inputs.intact module pypath.inputs.integrins module pypath.inputs.interpro module pypath.inputs.intogen module pypath.inputs.ipi module pypath.inputs.iptmnet module pypath.inputs.italk module pypath.inputs.kea module pypath.inputs.kegg module pypath.inputs.kegg_api module pypath.inputs.kinasedotcom module pypath.inputs.kirouac2010 module pypath.inputs.lambert2018 module pypath.inputs.laudanna module pypath.inputs.li2012 module pypath.inputs.lincs module pypath.inputs.lipidmaps module pypath.inputs.lipidmaps.structures module pypath.inputs.lmpid module pypath.inputs.lncdisease module pypath.inputs.lncrnadb module pypath.inputs.locate module pypath.inputs.lrdb module pypath.inputs.macrophage module pypath.inputs.main module pypath.inputs.matrisome module pypath.inputs.matrixdb module pypath.inputs.mcam module pypath.inputs.membranome module pypath.inputs.mimp module pypath.inputs.mir2disease module pypath.inputs.mirbase module pypath.inputs.mirdeathdb module pypath.inputs.mirecords module pypath.inputs.mirtarbase module pypath.inputs.mitab module pypath.inputs.mppi module pypath.inputs.msigdb module pypath.inputs.ncrdeathdb module pypath.inputs.negatome module pypath.inputs.netbiol module pypath.inputs.netpath module pypath.inputs.offsides module pypath.inputs.oma module pypath.inputs.ontology module pypath.inputs.opentargets module pypath.inputs.opm module pypath.inputs.oreganno module pypath.inputs.panglaodb module pypath.inputs.pathophenodb module pypath.inputs.pathwaycommons module pypath.inputs.pazar module pypath.inputs.pdb module pypath.inputs.pdzbase module pypath.inputs.pepcyber module pypath.inputs.pfam module pypath.inputs.pharos module pypath.inputs.phobius module pypath.inputs.phosphatome module pypath.inputs.phosphoelm module pypath.inputs.phosphonetworks module pypath.inputs.phosphopoint module pypath.inputs.phosphosite module pypath.inputs.pisa module pypath.inputs.pro module pypath.inputs.progeny module pypath.inputs.proteinatlas module pypath.inputs.proteins module pypath.inputs.protmapper module pypath.inputs.pubchem module pypath.inputs.pubmed module pypath.inputs.ramilowski2015 module pypath.inputs.ramp module pypath.inputs.rdata module pypath.inputs.reaction module pypath.inputs.reactome module pypath.inputs.scconnect module pypath.inputs.science module pypath.inputs.sider module pypath.inputs.signalink module pypath.inputs.signor module pypath.inputs.spike module pypath.inputs.stitch module pypath.inputs.string module pypath.inputs.surfaceome module pypath.inputs.swisslipids module pypath.inputs.switches_elm module pypath.inputs.talklr module pypath.inputs.tcdb module pypath.inputs.tfcensus module pypath.inputs.threedcomplex module pypath.inputs.threedid module pypath.inputs.topdb module pypath.inputs.transmir module pypath.inputs.trip module pypath.inputs.trrust module pypath.inputs.twosides module pypath.inputs.unichem module pypath.inputs.uniprot module pypath.inputs.uniprot_db module pypath.inputs.uniprot_idmapping module pypath.inputs.wang module pypath.inputs.wojtowicz2020 module pypath.inputs.zhong2015 module pypath.internals module pypath.internals.annot_formats module pypath.internals.input_formats module pypath.internals.intera module pypath.internals.license module pypath.internals.maps module pypath.internals.refs module pypath.internals.resource module pypath.legacy module pypath.legacy.db_categories module pypath.omnipath module pypath.omnipath.app module pypath.omnipath.databases module pypath.omnipath.databases.define module pypath.omnipath.export module pypath.omnipath.param module pypath.omnipath.server module pypath.omnipath.server.build module pypath.omnipath.server.generate_about_page module pypath.omnipath.server.legacy module pypath.omnipath.server.run module pypath.resources module pypath.resources.controller module pypath.resources.data module pypath.resources.data_formats module pypath.resources.descriptions module pypath.resources.licenses module pypath.resources.network module pypath.resources.urls module pypath.share module pypath.share.cache module pypath.share.common module pypath.share.constants module pypath.share.curl module pypath.share.progress module pypath.share.session module pypath.share.settings module pypath.utils module pypath.utils.go module pypath.utils.mapping module pypath.utils.metabo module pypath.utils.orthology module pypath.utils.pdb module pypath.utils.proteomicsdb module pypath.utils.pyreact module pypath.utils.reflists module pypath.utils.residues module pypath.utils.seq module pypath.utils.taxonomy module pypath.utils.unichem module pypath.utils.uniprot module pypath.visual module pypath.visual.drawing module pypath.visual.igraph_drawing module pypath.visual.igraph_drawing.edge module pypath.visual.igraph_drawing.vertex module PypathServer (class in pypath.omnipath.server.legacy) PyReact (class in pypath.utils.pyreact)

Q

quality_check_table() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method)

query() (in module pypath.utils.uniprot) (pypath.utils.proteomicsdb.ProteomicsDB method) query_builder() (in module pypath.inputs.uniprot)

R

Ramilowski2015 (class in pypath.core.annot) Ramilowski2015Location (class in pypath.core.annot) ramilowski_interactions() (in module pypath.inputs.ramilowski2015) ramilowski_locations() (in module pypath.inputs.ramilowski2015) RampMapping (class in pypath.internals.input_formats) random_interaction() (pypath.core.network.Network method) raw() (in module pypath.inputs.hmdb.common) (in module pypath.inputs.hmdb.metabolites) (in module pypath.inputs.hmdb.proteins) Reaction (class in pypath.utils.pyreact) reaction_pc (in module pypath.resources.data_formats) reactions_biopax() (in module pypath.inputs.reaction) ReactionSide (class in pypath.utils.pyreact) reactome_biopax() (in module pypath.inputs.reaction) reactome_bs() (in module pypath.inputs.reaction) reactome_chebis() (in module pypath.inputs.reactome) reactome_interactions() (in module pypath.inputs.reaction) reactome_pathway_relations() (in module pypath.inputs.reactome) reactome_pathways() (in module pypath.inputs.reactome) reactome_sbml() (in module pypath.inputs.reaction) reactome_uniprots() (in module pypath.inputs.reactome) read() (pypath.utils.mapping.MapReader method) read_cache() (pypath.utils.mapping.MapReader method) read_fasta() (in module pypath.utils.seq) read_mapping_array() (pypath.utils.mapping.MapReader method) read_mapping_biomart() (pypath.utils.mapping.MapReader method) read_mapping_file() (pypath.utils.mapping.MapReader method) read_mapping_hmdb() (pypath.utils.mapping.MapReader method) read_mapping_ramp() (pypath.utils.mapping.MapReader method) read_mapping_unichem() (pypath.utils.mapping.MapReader method) read_mapping_uniprot() (pypath.utils.mapping.MapReader method) read_mapping_uniprot_list() (pypath.utils.mapping.MapReader method) read_table() (in module pypath.inputs.common) read_xls() (in module pypath.inputs.common) ReadList (class in pypath.internals.input_formats) receiver (pypath.internals.annot_formats.AnnotDef attribute) receptor (pypath.inputs.cellinker.CellinkerInteraction attribute) (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute) (pypath.inputs.hpmr.HpmrInteraction attribute) (pypath.inputs.icellnet.IcellnetRecord attribute) receptor_class (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute) receptor_location (pypath.inputs.cellinker.CellinkerInteraction attribute) Reference (class in pypath.internals.refs) (class in pypath.utils.pyreact) ReferenceListManager (class in pypath.utils.reflists) references (pypath.core.interaction.InteractionDataFrameRecord attribute) (pypath.inputs.hpmr.HpmrInteraction attribute) (pypath.inputs.icellnet.IcellnetRecord attribute) (pypath.inputs.iptmnet.IptmnetInteraction attribute) (pypath.inputs.lrdb.LrdbAnnotation attribute) references_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) references_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) references_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) references_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) references_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) references_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) register() (pypath.utils.orthology.OrthologMeta method) register_network() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) regsites_tab() (in module pypath.inputs.phosphosite) regulated_by (pypath.core.network.Network attribute) regulates (pypath.core.network.Network attribute) Regulation (class in pypath.internals.intera) rel_type (pypath.utils.orthology.OmaOrtholog attribute) reload() (in module pypath.utils.uniprot) (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.AnnotationTable method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.CustomAnnotation method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOCustomIntercell method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) (pypath.core.complex.ComplexAggregator method) (pypath.core.evidence.Evidence method) (pypath.core.evidence.Evidences method) (pypath.core.interaction.Interaction method) (pypath.core.intercell.IntercellAnnotation method) (pypath.core.network.Network method) (pypath.omnipath.app.DatabaseManager method) (pypath.utils.go.GeneOntology method) (pypath.utils.go.GOAnnotation method) (pypath.utils.go.GOCustomAnnotation method) (pypath.utils.mapping.Mapper method)

reload_module() (pypath.omnipath.app.DatabaseManager method) RemoteFile (class in pypath.share.curl) remove_all() (pypath.omnipath.app.DatabaseManager method) remove_db() (pypath.omnipath.app.DatabaseManager method) remove_expired() (pypath.utils.mapping.Mapper method) remove_interaction() (pypath.core.network.Network method) remove_key() (pypath.utils.mapping.Mapper method) remove_loops() (pypath.core.network.Network method) remove_node() (pypath.core.network.Network method) remove_table() (pypath.utils.mapping.Mapper method) remove_xrefs() (in module pypath.utils.uniprot) remove_zero_degree() (pypath.core.network.Network method) replace_forbidden() (pypath.share.curl.Curl class method) replaced_by (pypath.inputs.uniprot.UniprotRecordHistory attribute) replaces (pypath.inputs.uniprot.UniprotRecordHistory attribute) resaa (pypath.inputs.iptmnet.IptmnetInteraction attribute) reset() (pypath.core.network.Network method) Residue (class in pypath.internals.intera) (class in pypath.utils.pdb) residue_1 (pypath.inputs.pisa.PisaBond attribute) residue_2 (pypath.inputs.pisa.PisaBond attribute) residue_pdb() (in module pypath.utils.pdb) ResidueMapper (class in pypath.utils.pdb) (class in pypath.utils.residues) resnum (pypath.inputs.iptmnet.IptmnetInteraction attribute) (pypath.utils.pdb.Residue attribute) Resource (class in pypath.utils.seq) resource (pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute) (pypath.internals.annot_formats.AnnotDef attribute) (pypath.internals.annot_formats.AnnotDefKey attribute) (pypath.utils.orthology.OrthologyTableKey attribute) resource_cat (pypath.core.network.NetworkStatsRecord attribute) resource_id_type() (pypath.internals.input_formats.UniprotMapping static method) (pypath.utils.mapping.MapReader method) resource_list_latex() (in module pypath.omnipath.server.generate_about_page) (in module pypath.resources.descriptions) resource_name (pypath.internals.annot_formats.AnnotDef attribute) resource_names (pypath.core.network.Network property) resource_names_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resource_names_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resource_names_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resource_names_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resource_names_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resource_names_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resource_names_via_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resource_names_via_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resource_names_via_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resource_names_via_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resource_names_via_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resource_names_via_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) ResourceAttributes (class in pypath.internals.resource) ResourceController (class in pypath.resources.controller) resources (pypath.core.network.Network property) (pypath.inputs.cellinker.CellinkerInteraction attribute) (pypath.inputs.icellnet.IcellnetRecord attribute) resources_a_b() (pypath.core.interaction.Interaction method) resources_b_a() (pypath.core.interaction.Interaction method) resources_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resources_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resources_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resources_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resources_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resources_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resources_in_category() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) resources_undirected() (pypath.core.interaction.Interaction method) resources_via_by_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resources_via_by_interaction_type (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resources_via_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resources_via_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resources_via_by_reference (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) resources_via_by_resource (pypath.core.interaction.Interaction attribute) (pypath.core.network.Network attribute) Rest (class in pypath.omnipath.server.run) reverse_key() (pypath.utils.mapping.Mapper method) reverse_mapping() (pypath.utils.mapping.Mapper static method) role (pypath.inputs.lrdb.LrdbAnnotation attribute) rolland_hi_ii_14() (in module pypath.inputs.huri)

S

save_to_pickle() (pypath.core.network.Network method) Scconnect (class in pypath.core.annot) scconnect_annotations() (in module pypath.inputs.scconnect) scconnect_complexes() (in module pypath.inputs.scconnect) scconnect_interactions() (in module pypath.inputs.scconnect) ScconnectComplex (class in pypath.core.annot) science_download() (in module pypath.inputs.science) scope (pypath.internals.annot_formats.AnnotDef attribute) score (pypath.inputs.iptmnet.IptmnetInteraction attribute) (pypath.utils.orthology.OmaOrtholog attribute) sdf() (in module pypath.inputs.hmdb.structures) (in module pypath.inputs.lipidmaps.structures) search() (pypath.core.annot.AnnotationTable method) secondary_resources() (pypath.resources.controller.ResourceController method) secreted (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute) secreted_class (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute) Segment (class in pypath.utils.pdb) select() (in module pypath.utils.reflists) (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.CustomAnnotation method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) (pypath.core.intercell.IntercellAnnotation method) (pypath.utils.go.GOAnnotation method) (pypath.utils.reflists.ReferenceListManager method) select_by_all() (pypath.utils.go.GOAnnotation method) select_by_expr() (pypath.utils.go.GOAnnotation method) select_by_expr_terms() (pypath.utils.go.GOAnnotation method) select_by_name() (pypath.utils.go.GOAnnotation method) select_by_term() (pypath.utils.go.GOAnnotation method) Seq (class in pypath.utils.seq) seqnum_1 (pypath.inputs.pisa.PisaBond attribute) seqnum_2 (pypath.inputs.pisa.PisaBond attribute) sequence (pypath.utils.uniprot.UniprotProtein property) sequence() (in module pypath.utils.uniprot) sequence_caution() (in module pypath.utils.uniprot) sequence_caution_with_xrefs() (in module pypath.utils.uniprot) sequence_version (pypath.inputs.uniprot.UniprotRecordHistory attribute) SequenceContainer (class in pypath.utils.orthology) serialize() (pypath.core.attrs.AttributeHandler method) (pypath.core.entity.Entity method) (pypath.core.evidence.Evidence method) (pypath.core.interaction.Interaction method) serialize_attrs() (pypath.core.evidence.Evidences method) (pypath.core.interaction.Interaction method) serialize_evidences() (pypath.core.interaction.Interaction method) set_binary_data() (pypath.share.curl.Curl method) set_done() (pypath.share.progress.Progress method) set_inputargs() (pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method) (pypath.core.enz_sub.EnzymeSubstrateProcessor method) set_interclass_network_df() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) set_method() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) (pypath.core.complex.AbstractComplexResource method) (pypath.core.complex.Cellchatdb method) (pypath.core.complex.Cellinker method) (pypath.core.complex.CellPhoneDB method) (pypath.core.complex.Compleat method) (pypath.core.complex.ComplexAggregator method) (pypath.core.complex.ComplexPortal method) (pypath.core.complex.Corum method) (pypath.core.complex.GuideToPharmacology method) (pypath.core.complex.Havugimana method) (pypath.core.complex.Hpmr method) (pypath.core.complex.Humap method) (pypath.core.complex.Humap2 method) (pypath.core.complex.Icellnet method) (pypath.core.complex.Kegg method) (pypath.core.complex.Pdb method) (pypath.core.complex.Signor method) (pypath.core.complex.Spike method) (pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method) (pypath.core.enz_sub.EnzymeSubstrateProcessor method) (pypath.internals.resource.AbstractResource method) set_network() (pypath.omnipath.app.DatabaseManager method) set_of() (pypath.utils.go.GeneOntology method) set_of_names() (pypath.utils.go.GeneOntology method) set_of_terms() (pypath.utils.go.GeneOntology method) set_progress() (pypath.utils.pyreact.BioPaxReader method) set_reference_set() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method)

set_status() (pypath.share.progress.Progress method) set_total() (pypath.share.progress.Progress method) set_uniprot_space() (pypath.utils.mapping.MapReader method) setdefault() (pypath.internals.resource.NetworkDataset method) setup_cache() (pypath.utils.mapping.MapReader method) shared (pypath.core.network.NetworkStatsRecord attribute) shared_cat (pypath.core.network.NetworkStatsRecord attribute) shared_res_cat (pypath.core.network.NetworkStatsRecord attribute) short_latin_names() (in module pypath.utils.taxonomy) shorten_latin_name() (in module pypath.utils.taxonomy) show() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.CustomAnnotation method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) (pypath.core.intercell.IntercellAnnotation method) show_structure() (in module pypath.inputs.hmdb.visual) side_effect (pypath.inputs.sider.SiderSideeffect attribute) (pypath.inputs.sider.SiderSideeffetFrequency attribute) side_effect_name (pypath.inputs.sider.SiderSideeffectMeddra attribute) sider_drug_names() (in module pypath.inputs.sider) sider_meddra_side_effects() (in module pypath.inputs.sider) sider_side_effect_frequencies() (in module pypath.inputs.sider) sider_side_effects() (in module pypath.inputs.sider) SiderDrug (class in pypath.inputs.sider) SiderSideeffect (class in pypath.inputs.sider) SiderSideeffectMeddra (class in pypath.inputs.sider) SiderSideeffetFrequency (class in pypath.inputs.sider) signalink_annotations() (in module pypath.inputs.signalink) signalink_function_annotations() (in module pypath.inputs.signalink) signalink_interactions() (in module pypath.inputs.signalink) signalink_pathway_annotations() (in module pypath.inputs.signalink) SignalinkFunctions (class in pypath.core.annot) SignalinkPathways (class in pypath.core.annot) Signor (class in pypath.core.complex) signor_complexes() (in module pypath.inputs.signor) signor_enzyme_substrate() (in module pypath.inputs.signor) signor_interactions() (in module pypath.inputs.signor) signor_pathway_annotations() (in module pypath.inputs.signor) signor_pathways() (in module pypath.inputs.signor) signor_protein_families() (in module pypath.inputs.signor) SignorPathways (class in pypath.core.annot) similarity() (in module pypath.utils.uniprot) similarity_with_xrefs() (in module pypath.utils.uniprot) simple_dict (pypath.core.evidence.Evidences property) small_molecule_identifiers_by_data_model (pypath.core.network.Network attribute) small_molecule_identifiers_by_data_model() (pypath.core.interaction.Interaction method) small_molecule_identifiers_by_interaction_type (pypath.core.network.Network attribute) small_molecule_identifiers_by_interaction_type() (pypath.core.interaction.Interaction method) small_molecule_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute) small_molecule_identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) small_molecule_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) small_molecule_identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) small_molecule_identifiers_by_reference (pypath.core.network.Network attribute) small_molecule_identifiers_by_reference() (pypath.core.interaction.Interaction method) small_molecule_identifiers_by_resource (pypath.core.network.Network attribute) small_molecule_identifiers_by_resource() (pypath.core.interaction.Interaction method) small_molecule_labels_by_data_model (pypath.core.network.Network attribute) small_molecule_labels_by_data_model() (pypath.core.interaction.Interaction method) small_molecule_labels_by_interaction_type (pypath.core.network.Network attribute) small_molecule_labels_by_interaction_type() (pypath.core.interaction.Interaction method) small_molecule_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute) small_molecule_labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) small_molecule_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) small_molecule_labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) small_molecule_labels_by_reference (pypath.core.network.Network attribute) small_molecule_labels_by_reference() (pypath.core.interaction.Interaction method) small_molecule_labels_by_resource (pypath.core.network.Network attribute) small_molecule_labels_by_resource() (pypath.core.interaction.Interaction method) small_molecules_by_data_model (pypath.core.network.Network attribute) small_molecules_by_data_model() (pypath.core.interaction.Interaction method) small_molecules_by_interaction_type (pypath.core.network.Network attribute) small_molecules_by_interaction_type() (pypath.core.interaction.Interaction method) small_molecules_by_interaction_type_and_data_model (pypath.core.network.Network attribute) small_molecules_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method) small_molecules_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute) small_molecules_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method) small_molecules_by_reference (pypath.core.network.Network attribute) small_molecules_by_reference() (pypath.core.interaction.Interaction method) small_molecules_by_resource (pypath.core.network.Network attribute) small_molecules_by_resource() (pypath.core.interaction.Interaction method) smiles2chembl() (pypath.utils.unichem.Unichem method) source (pypath.internals.annot_formats.AnnotDef attribute) (pypath.utils.orthology.OrthologyTableKey attribute) source() (pypath.core.interaction.Interaction method) sources (pypath.core.interaction.InteractionDataFrameRecord attribute) (pypath.inputs.lrdb.LrdbAnnotation attribute) sources_reverse() (pypath.core.interaction.Interaction method) sources_straight() (pypath.core.interaction.Interaction method) sources_table() (pypath.omnipath.export.Export class method) sources_undirected() (pypath.core.interaction.Interaction method) Spike (class in pypath.core.complex) spike_complexes() (in module pypath.inputs.spike) spike_interactions() (in module pypath.inputs.spike) src() (pypath.core.interaction.Interaction method) src_by_resource() (pypath.core.interaction.Interaction method) step() (pypath.share.progress.Progress method) stitch_actions_interactions() (in module pypath.inputs.stitch) stitch_links_interactions() (in module pypath.inputs.stitch) stop_server() (in module pypath.omnipath.server.run) string_effects() (in module pypath.inputs.string) string_links_interactions() (in module pypath.inputs.string) string_physical_interactions() (in module pypath.inputs.string) string_species() (in module pypath.inputs.string) structure_svg() (in module pypath.inputs.hmdb.visual) subcellular_location() (in module pypath.utils.uniprot) subcellular_location_with_xrefs() (in module pypath.utils.uniprot) subfamily (pypath.inputs.icellnet.IcellnetRecord attribute) subgraph_nodes() (pypath.utils.go.GeneOntology method) subset_intersection() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) substrate (pypath.inputs.iptmnet.IptmnetInteraction attribute) substrate_isoform (pypath.inputs.iptmnet.IptmnetInteraction attribute) subunit() (in module pypath.utils.uniprot) subunit_with_xrefs() (in module pypath.utils.uniprot) summaries_tab() (pypath.core.network.Network method) suppressed_by (pypath.core.network.Network attribute) suppresses (pypath.core.network.Network attribute) Surfaceome (class in pypath.core.annot) surfaceome_annotations() (in module pypath.inputs.surfaceome) swissprot_deleted() (in module pypath.inputs.uniprot) swissprot_seq() (in module pypath.utils.seq) swissprots() (pypath.utils.mapping.Mapper method) synonyms (pypath.inputs.adrecs.AdrecsDrug attribute) (pypath.inputs.adrecs.AdrecsTerm attribute)

T

table() (in module pypath.inputs.hmdb.common) (in module pypath.inputs.hmdb.metabolites) (in module pypath.inputs.hmdb.proteins) table_path() (pypath.omnipath.app.DatabaseManager method) tables_loaded() (pypath.utils.mapping.MapReader method) TableServer (class in pypath.omnipath.server.run) take_a_trip() (in module pypath.inputs.trip) Talklr (class in pypath.core.annot) talklr_annotations() (in module pypath.inputs.talklr) talklr_interactions() (in module pypath.inputs.talklr) talklr_raw() (in module pypath.inputs.talklr) TaperedEdgeDrawer (class in pypath.visual.igraph_drawing.edge) target (pypath.inputs.dorothea.DorotheaInteraction attribute) (pypath.utils.orthology.OrthologyTableKey attribute) target() (pypath.core.interaction.Interaction method) target_id_type (pypath.utils.mapping.MappingTableKey attribute) taxid_from_common_name() (in module pypath.utils.taxonomy) taxid_from_dbptm_taxon_name() (in module pypath.utils.taxonomy) taxid_from_ensembl_name() (in module pypath.utils.taxonomy) taxid_from_latin_name() (in module pypath.utils.taxonomy) taxid_from_nonstandard() (in module pypath.utils.taxonomy) Taxon (class in pypath.inputs.uniprot) taxon (pypath.core.entity.EntityKey attribute) Tcdb (class in pypath.core.annot) tcdb_annotations() (in module pypath.inputs.tcdb) tcdb_classes() (in module pypath.inputs.tcdb) tcdb_families() (in module pypath.inputs.tcdb) tdd (pypath.inputs.adrecs.AdrecsDrug attribute) terminate() (pypath.share.progress.Progress method) terms_to_names() (pypath.utils.go.GeneOntology method) terms_to_names_aspects() (pypath.utils.go.GeneOntology method) TextDrawer (in module pypath.visual.igraph_drawing) textmining_filtered() (in module pypath.inputs.diseases) textmining_full() (in module pypath.inputs.diseases) tf (pypath.inputs.dorothea.DorotheaInteraction attribute) tf_target_resources() (in module pypath.omnipath.param) Tfcensus (class in pypath.core.annot) tfcensus_annotations() (in module pypath.inputs.tfcensus) tfregulons_interactions() (in module pypath.inputs.dorothea) tfregulons_interactions_old() (in module pypath.inputs.dorothea) tgt() (pypath.core.interaction.Interaction method) tgt_by_resource() (pypath.core.interaction.Interaction method) threedcomplex_chains() (in module pypath.inputs.threedcomplex) threedcomplex_complexes() (in module pypath.inputs.threedcomplex) threedcomplex_contacts() (in module pypath.inputs.threedcomplex) threedcomplex_ddi() (in module pypath.inputs.threedcomplex) threedcomplex_nresidues() (in module pypath.inputs.threedcomplex) throughput (pypath.inputs.gutmgene.GutmgeneAnnotation attribute) (pypath.inputs.gutmgene.GutmgeneRaw attribute) tissue_specificity() (in module pypath.utils.uniprot) tissue_specificity_with_xrefs() (in module pypath.utils.uniprot) tissues_x_proteins() (pypath.utils.proteomicsdb.ProteomicsDB method) to_array() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) to_bool_array() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method)

to_igraph() (pypath.core.network.Network method) to_int() (pypath.internals.license.LicenseAttrib method) (pypath.internals.license.LicenseFeature method) (pypath.internals.license.LicensePurpose method) (pypath.internals.license.LicenseSharing method) to_set() (pypath.core.annot.Adhesome method) (pypath.core.annot.Almen2009 method) (pypath.core.annot.AnnotationBase method) (pypath.core.annot.Baccin2019 method) (pypath.core.annot.Biogps method) (pypath.core.annot.Cancerdrugsdb method) (pypath.core.annot.CancerGeneCensus method) (pypath.core.annot.Cancersea method) (pypath.core.annot.Cellcall method) (pypath.core.annot.Cellcellinteractions method) (pypath.core.annot.Cellchatdb method) (pypath.core.annot.CellchatdbComplex method) (pypath.core.annot.Cellinker method) (pypath.core.annot.CellinkerComplex method) (pypath.core.annot.CellPhoneDB method) (pypath.core.annot.CellPhoneDBComplex method) (pypath.core.annot.CellSurfaceProteinAtlas method) (pypath.core.annot.CellSurfaceProteinAtlasCellType method) (pypath.core.annot.Celltalkdb method) (pypath.core.annot.Celltypist method) (pypath.core.annot.Comppi method) (pypath.core.annot.Connectomedb method) (pypath.core.annot.Corum method) (pypath.core.annot.CorumFuncat method) (pypath.core.annot.CorumGO method) (pypath.core.annot.Cpad method) (pypath.core.annot.Cytosig method) (pypath.core.annot.Dgidb method) (pypath.core.annot.Disgenet method) (pypath.core.annot.Embrace method) (pypath.core.annot.Exocarta method) (pypath.core.annot.GOIntercell method) (pypath.core.annot.Gpcrdb method) (pypath.core.annot.GuideToPharmacology method) (pypath.core.annot.Hgnc method) (pypath.core.annot.HpmrComplex method) (pypath.core.annot.HPO method) (pypath.core.annot.Humancellmap method) (pypath.core.annot.HumanPlasmaMembraneReceptome method) (pypath.core.annot.HumanProteinAtlas method) (pypath.core.annot.HumanProteinAtlasSecretome method) (pypath.core.annot.HumanProteinAtlasSubcellular method) (pypath.core.annot.Icellnet method) (pypath.core.annot.IcellnetComplex method) (pypath.core.annot.Integrins method) (pypath.core.annot.InterPro method) (pypath.core.annot.Intogen method) (pypath.core.annot.Italk method) (pypath.core.annot.KeggPathways method) (pypath.core.annot.KeggPathwaysPC method) (pypath.core.annot.Kinasedotcom method) (pypath.core.annot.Kirouac2010 method) (pypath.core.annot.Lambert2018 method) (pypath.core.annot.LigandReceptor method) (pypath.core.annot.Locate method) (pypath.core.annot.Lrdb method) (pypath.core.annot.Matrisome method) (pypath.core.annot.Matrixdb method) (pypath.core.annot.Mcam method) (pypath.core.annot.Membranome method) (pypath.core.annot.Msigdb method) (pypath.core.annot.NetpathPathways method) (pypath.core.annot.Opm method) (pypath.core.annot.Panglaodb method) (pypath.core.annot.Phobius method) (pypath.core.annot.Phosphatome method) (pypath.core.annot.Progeny method) (pypath.core.annot.Ramilowski2015 method) (pypath.core.annot.Ramilowski2015Location method) (pypath.core.annot.Scconnect method) (pypath.core.annot.ScconnectComplex method) (pypath.core.annot.SignalinkFunctions method) (pypath.core.annot.SignalinkPathways method) (pypath.core.annot.SignorPathways method) (pypath.core.annot.Surfaceome method) (pypath.core.annot.Talklr method) (pypath.core.annot.Tcdb method) (pypath.core.annot.Tfcensus method) (pypath.core.annot.Topdb method) (pypath.core.annot.UniprotFamilies method) (pypath.core.annot.UniprotKeywords method) (pypath.core.annot.UniprotLocations method) (pypath.core.annot.UniprotTissues method) (pypath.core.annot.UniprotTopologies method) (pypath.core.annot.Vesiclepedia method) (pypath.core.annot.Wang method) (pypath.core.annot.Zhong2015 method) Topdb (class in pypath.core.annot) topdb_annotations() (in module pypath.inputs.topdb) total (pypath.core.network.NetworkStatsRecord attribute) transcription() (pypath.core.network.Network class method) transcription_deprecated (in module pypath.resources.data_formats) transcription_onebyone (in module pypath.resources.data_formats) transcriptionally_activated_by (pypath.core.network.Network attribute) transcriptionally_activates (pypath.core.network.Network attribute) transcriptionally_regulated_by (pypath.core.network.Network attribute) transcriptionally_regulates (pypath.core.network.Network attribute) transcriptionally_suppressed_by (pypath.core.network.Network attribute) transcriptionally_suppresses (pypath.core.network.Network attribute) translate() (in module pypath.utils.orthology) (pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method) (pypath.core.interaction.Interaction method) (pypath.utils.orthology.EnsemblOrthology method) (pypath.utils.orthology.HomologeneOrthology method) (pypath.utils.orthology.OmaOrthology method) (pypath.utils.orthology.OrthologyManager method) (pypath.utils.orthology.ProteinOrthology method) (pypath.utils.orthology.PtmOrthology method) (pypath.utils.unichem.Unichem method) translate_deleted_uniprot_by_genesymbol() (pypath.utils.mapping.Mapper method) translate_df() (in module pypath.utils.orthology) (pypath.utils.orthology.EnsemblOrthology method) (pypath.utils.orthology.HomologeneOrthology method) (pypath.utils.orthology.OmaOrthology method) (pypath.utils.orthology.OrthologyManager method) (pypath.utils.orthology.ProteinOrthology method) translate_site() (pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method) (pypath.utils.orthology.PtmOrthology method) translation_df() (in module pypath.utils.mapping) (pypath.utils.mapping.Mapper method) translation_dict() (in module pypath.utils.mapping) (pypath.utils.mapping.Mapper method) transmembrane (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute) transmir_interactions() (in module pypath.inputs.transmir) transmitter (pypath.internals.annot_formats.AnnotDef attribute) trembl_deleted() (in module pypath.inputs.uniprot) trembl_swissprot() (pypath.utils.mapping.Mapper method) trip_find_uniprot() (in module pypath.inputs.trip) trip_get_uniprot() (in module pypath.inputs.trip) trip_interactions() (in module pypath.inputs.trip) trip_process() (in module pypath.inputs.trip) trip_process_table() (in module pypath.inputs.trip) trrust_human() (in module pypath.inputs.trrust) trrust_interactions() (in module pypath.inputs.trrust) trrust_mouse() (in module pypath.inputs.trrust) twisted_listen_tcp() (in module pypath.omnipath.server.run) twisted_run() (in module pypath.omnipath.server.run) TwistedWebResource (class in pypath.omnipath.server.run) TwistedWebSite (class in pypath.omnipath.server.run) twosides_interactions() (in module pypath.inputs.twosides) type (pypath.core.interaction.InteractionDataFrameRecord attribute) (pypath.inputs.cellinker.CellinkerInteraction attribute) type_a (pypath.core.interaction.InteractionDataFrameRecord attribute) type_b (pypath.core.interaction.InteractionDataFrameRecord attribute) types (pypath.utils.orthology.EnsemblOrtholog attribute)

U

umls_concept_in_meddra (pypath.inputs.sider.SiderSideeffect attribute) (pypath.inputs.sider.SiderSideeffetFrequency attribute) umls_concept_on_label (pypath.inputs.sider.SiderSideeffect attribute) (pypath.inputs.sider.SiderSideeffetFrequency attribute) unambiguous (pypath.inputs.hpmr.HpmrInteraction attribute) Unichem (class in pypath.utils.unichem) unichem_info() (in module pypath.inputs.unichem) unichem_mapping() (in module pypath.inputs.unichem) unichem_sources() (in module pypath.inputs.unichem) UnichemMapping (class in pypath.internals.input_formats) uniprot (pypath.utils.pdb.Residue attribute) (pypath.utils.pdb.Segment attribute) uniprot_1 (pypath.inputs.pisa.PisaBond attribute) uniprot_2 (pypath.inputs.pisa.PisaBond attribute) uniprot_cleanup() (pypath.utils.mapping.Mapper method) uniprot_data() (in module pypath.inputs.uniprot) uniprot_deleted() (in module pypath.inputs.uniprot) uniprot_end (pypath.utils.pdb.Segment attribute) uniprot_families() (in module pypath.inputs.uniprot) uniprot_history() (in module pypath.inputs.uniprot) uniprot_history_recent_datasheet() (in module pypath.inputs.uniprot) UNIPROT_ID_TYPES (in module pypath.utils.mapping) uniprot_keywords() (in module pypath.inputs.uniprot) uniprot_locations() (in module pypath.inputs.uniprot) uniprot_ncbi_taxids() (in module pypath.inputs.uniprot) uniprot_ncbi_taxids_2() (in module pypath.inputs.uniprot) uniprot_preprocess() (in module pypath.inputs.uniprot) uniprot_query() (in module pypath.inputs.uniprot) uniprot_recent_version() (in module pypath.inputs.uniprot) uniprot_start (pypath.utils.pdb.Segment attribute) uniprot_taxid() (in module pypath.utils.taxonomy) uniprot_taxonomy() (in module pypath.inputs.uniprot) uniprot_tissues() (in module pypath.inputs.uniprot) uniprot_topology() (in module pypath.inputs.uniprot) uniprot_variants() (in module pypath.inputs.humsavar)

UniprotFamilies (class in pypath.core.annot) UniprotKeywords (class in pypath.core.annot) UniprotListMapping (class in pypath.internals.input_formats) UniprotLocations (class in pypath.core.annot) UniprotMapping (class in pypath.internals.input_formats) UniprotProtein (class in pypath.utils.uniprot) UniprotQuery (class in pypath.inputs.uniprot) UniprotRecordHistory (class in pypath.inputs.uniprot) UniprotTissues (class in pypath.core.annot) UniprotTopologies (class in pypath.core.annot) unique (pypath.core.network.NetworkStatsRecord attribute) unique() (pypath.core.enz_sub.EnzymeSubstrateAggregator method) unique_cat (pypath.core.network.NetworkStatsRecord attribute) unique_res_cat (pypath.core.network.NetworkStatsRecord attribute) unload() (pypath.utils.seq.Pfam method) (pypath.utils.seq.Resource method) unset_dir() (pypath.core.interaction.Interaction method) unset_direction() (pypath.core.interaction.Interaction method) unset_interaction_type() (pypath.core.interaction.Interaction method) unset_sign() (pypath.core.interaction.Interaction method) update() (pypath.internals.resource.NetworkDataset method) (pypath.resources.controller.ResourceController method) update_attrs() (pypath.core.attrs.AttributeHandler method) (pypath.core.entity.Entity method) (pypath.core.evidence.Evidence method) (pypath.core.interaction.Interaction method) update_databases() (in module pypath.utils.uniprot) update_info() (in module pypath.utils.uniprot) update_parents() (pypath.core.annot.CustomAnnotation method) (pypath.core.intercell.IntercellAnnotation method) url (pypath.inputs.biogps.BiogpsDataset attribute) (pypath.inputs.uniprot.UniprotQuery property) url_fix() (pypath.share.curl.Curl method) url_plain (pypath.inputs.uniprot.UniprotQuery property) usage() (pypath.utils.unichem.Unichem method)

V

valid_uniprot() (in module pypath.inputs.uniprot) (pypath.utils.mapping.Mapper method) values() (pypath.internals.resource.NetworkDataset method) variants() (in module pypath.inputs.proteins)

version (pypath.inputs.pathwaycommons.PathwayCommonsResource attribute) Vesiclepedia (class in pypath.core.annot) via (pypath.internals.resource.EnzymeSubstrateResourceKey attribute) (pypath.internals.resource.NetworkResourceKey attribute) vidal_hi_iii_old() (in module pypath.inputs.huri)

W

Wang (class in pypath.core.annot) wang_annotations() (in module pypath.inputs.wang) wang_interactions() (in module pypath.inputs.wang) web_resource() (in module pypath.utils.uniprot) web_resource_with_xrefs() (in module pypath.utils.uniprot) WebserviceTables (class in pypath.omnipath.server.build) weight (pypath.utils.uniprot.UniprotProtein property) weight() (in module pypath.utils.uniprot) weights (pypath.utils.uniprot.UniprotProtein property) weights() (in module pypath.utils.uniprot)

which_directions() (pypath.core.interaction.Interaction method) which_dirs() (pypath.core.interaction.Interaction method) which_signs() (pypath.core.interaction.Interaction method) which_table() (pypath.utils.mapping.Mapper method) wojtowicz2020_interactions() (in module pypath.inputs.wojtowicz2020) wojtowicz2020_raw() (in module pypath.inputs.wojtowicz2020) write_cache() (pypath.utils.mapping.MapReader method) write_html() (in module pypath.omnipath.server.generate_about_page) (in module pypath.resources.descriptions) write_tab() (pypath.omnipath.export.Export method)

Y

yang2016_interactions() (in module pypath.inputs.huri)

yu2011_interactions() (in module pypath.inputs.huri)

Z

Zhong2015 (class in pypath.core.annot)

zhong2015_annotations() (in module pypath.inputs.zhong2015)