Index

A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | Z

A

acsn_ppi() (in module pypath.dataio)
add_residues() (pypath.intera.Interface method)
add_update_vertex() (pypath.main.PyPath method)
all_between() (pypath.main.PyPath method)
apply_list() (pypath.main.PyPath method)
attach_network() (pypath.main.PyPath method)
AttributeHandler (class in pypath.pyreact)

B

BarplotsGrid (class in pypath.plot)
basic_stats() (pypath.main.PyPath method)
biogrid_interactions() (in module pypath.dataio)
biopax_size() (pypath.pyreact.BioPaxReader method), [1]
BioPaxReader (class in pypath.pyreact), [1]
bond_types() (pypath.intera.Interface method)
by_plot() (pypath.plot.MultiBarplot method)

C

cache_delete_off (class in pypath.curl)
cache_delete_on (class in pypath.curl)
cache_off (class in pypath.curl)
cache_on (class in pypath.curl)
cache_print_off (class in pypath.curl)
cache_print_on (class in pypath.curl)
cancer_gene_census_list() (pypath.main.PyPath method)
Chembl (class in pypath.chembl)
clean() (pypath.dataio.ResidueMapper method)
(pypath.pdb.ResidueMapper method), [1]
clean_graph() (pypath.main.PyPath method)
cleanDict() (in module pypath.common)
cleanup_hook() (pypath.pyreact.BioPaxReader method), [1]
close_biopax() (pypath.pyreact.BioPaxReader method), [1]
collapse_by_name() (pypath.main.PyPath method)
combine_attr() (pypath.main.PyPath method)
Complex (class in pypath.pyreact)
ComplexVariations (class in pypath.pyreact)
consensus_edges() (pypath.main.Direction method)
construct_binary_data() (pypath.curl.Curl method), [1]
Control (class in pypath.pyreact)
copy_edges() (pypath.main.PyPath method)
count_sol() (pypath.main.PyPath method)
curation_effort() (pypath.main.PyPath method)
CurationPlot (class in pypath.plot)
Curl (class in pypath.curl), [1]

D

delete_by_taxon() (pypath.main.PyPath method)
delete_unknown() (pypath.main.PyPath method)
Dendrogram (class in pypath.plot)
dgenesymbol() (pypath.main.PyPath method)
dgs() (pypath.main.PyPath method)
dip_login() (in module pypath.dataio)
Direction (class in pypath.main)
disease_genes_list() (pypath.main.PyPath method)
do_plot() (pypath.plot.MultiBarplot method)
Domain (class in pypath.intera)
DomainDomain (class in pypath.intera)
DomainMotif (class in pypath.intera)
dp() (pypath.main.PyPath method)
dprotein() (pypath.main.PyPath method)
druggability_list() (pypath.main.PyPath method)
dryrun_off (class in pypath.curl)
dryrun_on (class in pypath.curl)
duniprot() (pypath.main.PyPath method)
duniprots() (pypath.main.PyPath method)
dup() (pypath.main.PyPath method)
dups() (pypath.main.PyPath method)

E

edge_exists() (pypath.main.PyPath method)
edges_expression() (pypath.main.PyPath method)
edges_in_comlexes() (pypath.main.PyPath method)
Enrichment (class in pypath.enrich)
EnrichmentSet (class in pypath.enrich)
Entity (class in pypath.pyreact)
EntitySet (class in pypath.pyreact)
expand() (pypath.pyreact.Entity method)
(pypath.pyreact.ReactionSide method)
export_dot() (pypath.main.PyPath method)
export_edgelist() (pypath.main.PyPath method)
extract() (pypath.pyreact.BioPaxReader method), [1]

F

FileMapping (class in pypath.input_formats)
FileOpener (class in pypath.curl), [1]
find_all_paths() (pypath.main.PyPath method)
finish() (pypath.plot.BarplotsGrid method)
(pypath.plot.CurationPlot method)
(pypath.plot.Dendrogram method)
(pypath.plot.HtpCharacteristics method)
(pypath.plot.MultiBarplot method)
(pypath.plot.Plot method)
(pypath.plot.RefsComposite method)
(pypath.plot.ScatterPlus method)
(pypath.plot.StackedBarplot method)
flatten() (in module pypath.colorgen)

G

gen_cvariations() (pypath.pyreact.PyReact method)
genesymbol() (pypath.main.PyPath method)
genesymbol_labels() (pypath.main.PyPath method)
get_acsn_effects() (in module pypath.dataio)
get_bonds() (pypath.intera.Interface method)
get_ca1() (in module pypath.dataio)
get_ccmap() (in module pypath.dataio)
get_complexportal() (in module pypath.dataio)
get_dbptm() (in module pypath.dataio)
get_dgidb() (in module pypath.dataio)
get_dir() (pypath.main.Direction method)
get_directed() (pypath.main.PyPath method)
get_dirs() (pypath.main.Direction method)
get_disgenet() (in module pypath.dataio)
get_domino_ptms() (in module pypath.dataio)
get_edge() (pypath.main.PyPath method)
get_elm_interactions() (in module pypath.dataio)
get_giant() (pypath.main.PyPath method)
get_graphviz_attrs() (in module pypath.dataio)
get_guide2pharma() (in module pypath.dataio)
get_havugimana() (in module pypath.dataio)
get_homologene() (in module pypath.dataio)
get_hpmr() (in module pypath.dataio)
get_hprd() (in module pypath.dataio)
get_hprd_ptms() (in module pypath.dataio)
get_hsn() (in module pypath.dataio)
get_i3d() (in module pypath.dataio)
get_instruct() (in module pypath.dataio)
get_instruct_offsets() (in module pypath.dataio)
get_kegg() (in module pypath.dataio)
get_kinases() (in module pypath.dataio)
get_laudanna_directions() (in module pypath.dataio)
get_laudanna_effects() (in module pypath.dataio)
get_li2012() (in module pypath.dataio)
get_lit_bm_13() (in module pypath.dataio)
get_phosphoelm() (in module pypath.dataio)
get_phosphosite() (in module pypath.dataio)
get_phosphosite_curated() (in module pypath.dataio)
get_phosphosite_noref() (in module pypath.dataio)
get_pmid() (in module pypath.dataio)
get_qid() (pypath.mysql.MysqlRunner method)
get_switches_elm() (in module pypath.dataio)
get_tfcensus() (in module pypath.dataio)
get_wang_effects() (in module pypath.dataio)
getfracs() (in module pypath.colorgen)
GOAnnotation (class in pypath.go)
GOEnrichmentSet (class in pypath.go)
gs() (pypath.main.PyPath method)
gs_edge() (pypath.main.PyPath method)
GSEA (class in pypath.gsea)
GSEABinaryEnrichmentSet (class in pypath.gsea)

H

Histogram (class in pypath.plot)
HistoryTree (class in pypath.plot)
homologene_dict() (in module pypath.dataio)
hprd_interactions() (in module pypath.dataio)
HtpCharacteristics (class in pypath.plot)

I

in_same_component() (pypath.pyreact.PyReact method)
init_edge_attr() (pypath.main.PyPath method)
init_etree() (pypath.pyreact.BioPaxReader method), [1]
init_fig() (pypath.plot.BarplotsGrid method)
(pypath.plot.CurationPlot method)
(pypath.plot.Dendrogram method)
(pypath.plot.HtpCharacteristics method)
(pypath.plot.MultiBarplot method)
(pypath.plot.RefsComposite method)
(pypath.plot.ScatterPlus method)
(pypath.plot.StackedBarplot method)
init_network() (pypath.main.PyPath method)
init_vertex_attr() (pypath.main.PyPath method)
Interface (class in pypath.intera)
intogen_cancer_drivers_list() (pypath.main.PyPath method)
is_opentype_cff_font() (in module pypath.plot)
is_quoted() (pypath.curl.Curl method), [1]
iterate() (pypath.pyreact.BioPaxReader method), [1]
itermembers() (pypath.pyreact.ComplexVariations method)

K

kinases_list() (pypath.main.PyPath method)

L

labels() (pypath.plot.MultiBarplot method)
li2012_dmi() (in module pypath.dataio)
li2012_interactions() (in module pypath.dataio)
li2012_phospho() (in module pypath.dataio)
lmpid_dmi() (in module pypath.dataio)
lmpid_interactions() (in module pypath.dataio)
load_compleat() (pypath.main.PyPath method)
load_complexportal() (pypath.main.PyPath method)
load_corum() (pypath.main.PyPath method)
load_ddi() (pypath.main.PyPath method)
load_dmi() (pypath.main.PyPath method)
load_expression() (pypath.main.PyPath method)
load_go() (in module pypath.go)
load_havugimana() (pypath.main.PyPath method)
load_lmpid() (in module pypath.dataio)
load_macrophage() (in module pypath.dataio)
load_mappings() (pypath.mapping.Mapper method)
load_mutations() (pypath.main.PyPath method)
load_resources() (pypath.main.PyPath method)
load_signor_ptms() (in module pypath.dataio)
load_uniprot_mapping() (pypath.mapping.Mapper method)

M

majority_dir() (pypath.main.Direction method)
majority_sign() (pypath.main.Direction method)
make_plots() (pypath.plot.MultiBarplot method)
map_edge() (pypath.main.PyPath method)
map_item() (pypath.main.PyPath method)
map_list() (pypath.main.PyPath method)
map_name() (pypath.mapping.Mapper method)
Mapper (class in pypath.mapping)
MappingTable (class in pypath.mapping), [1]
md5() (in module pypath.common)
merge_complexes() (pypath.pyreact.PyReact method)
merge_cvariations() (pypath.pyreact.PyReact method)
merge_lists() (pypath.main.PyPath method)
merge_nodes() (pypath.main.PyPath method)
Motif (class in pypath.intera)
MultiBarplot (class in pypath.plot)
mutated_edges() (pypath.main.PyPath method)
Mutation (class in pypath.intera)
MysqlConnect (class in pypath.mysql_connect)
MysqlMapping (class in pypath.input_formats)
MysqlRunner (class in pypath.mysql)

N

network_filter() (pypath.main.PyPath method)
network_stats() (pypath.main.PyPath method)
numof_residues() (pypath.intera.Interface method)

O

only_pmids() (in module pypath.dataio)
open_biopax() (pypath.pyreact.BioPaxReader method), [1]
open_pubmed() (in module pypath.dataio)
orthology_translation() (pypath.main.PyPath method)

P

p() (pypath.main.PyPath method)
phosphosite_directions() (in module pypath.dataio)
PickleMapping (class in pypath.input_formats)
Plot (class in pypath.drawing)
(class in pypath.plot)
plot() (pypath.plot.MultiBarplot method)
(pypath.plot.StackedBarplot method)
plots_order() (pypath.plot.MultiBarplot method)
post_plot() (pypath.plot.MultiBarplot method)
pre_plot() (pypath.plot.MultiBarplot method)
preserve_off (class in pypath.curl)
preserve_on (class in pypath.curl)
primary_uniprot() (pypath.mapping.Mapper method)
process() (pypath.pyreact.BioPaxReader method), [1]
process_dmi() (pypath.main.PyPath method)
Progress (class in pypath.progress)
Protein (class in pypath.pyreact)
protein() (pypath.main.PyPath method)
protein_edge() (pypath.main.PyPath method)
ProteinFamily (class in pypath.pyreact)
proteome_list() (pypath.main.PyPath method)
ProteomicsDB (class in pypath.proteomicsdb)
Ptm (class in pypath.intera)
PyPath (class in pypath.main)
pypath.analysis (module)
pypath.chembl (module)
pypath.colorgen (module)
pypath.common (module)
pypath.curl (module)
pypath.dataio (module)
pypath.drawing (module)
pypath.enrich (module)
pypath.go (module)
pypath.gsea (module)
pypath.input_formats (module)
pypath.intera (module)
pypath.logn (module)
pypath.main (module)
pypath.mapping (module)
pypath.mapping_input (module)
pypath.maps (module)
pypath.moduland (module)
pypath.mysql (module)
pypath.mysql_connect (module)
pypath.pdb (module)
pypath.plot (module)
pypath.progress (module)
pypath.proteomicsdb (module)
pypath.pyreact (module)
pypath.reflists (module)
pypath.seq (module)
pypath.server (module)
pypath.unichem (module)
pypath.uniprot_input (module)
PyReact (class in pypath.pyreact)

R

randn() (in module pypath.plot)
Reaction (class in pypath.pyreact)
reactions_biopax() (in module pypath.dataio)
ReactionSide (class in pypath.pyreact)
reactome_biopax() (in module pypath.dataio)
reactome_interactions() (in module pypath.dataio)
reactome_sbml() (in module pypath.dataio)
read_complexes_havugimana() (in module pypath.dataio)
read_data_file() (pypath.main.PyPath method)
read_mapping_uniprot() (pypath.mapping.MappingTable method)
read_table() (in module pypath.dataio)
read_xls() (in module pypath.dataio)
ReadList (class in pypath.input_formats)
ReadSettings (class in pypath.input_formats)
receptors_list() (pypath.main.PyPath method)
Reference (class in pypath.refs)
ReferenceList (class in pypath.reflists)
refs (in module pypath)
RefsComposite (class in pypath.plot)
reload() (pypath.plot.MultiBarplot method)
(pypath.plot.ScatterPlus method)
(pypath.plot.StackedBarplot method)
Residue (class in pypath.intera)
ResidueMapper (class in pypath.dataio)
(class in pypath.pdb), [1]
Rest (class in pypath.server)
RestResource (class in pypath.server)
rolland_hi_ii_14() (in module pypath.dataio)
rotate() (in module pypath.common)
run_latex() (pypath.plot.HistoryTree method)

S

save_session() (pypath.main.PyPath method)
ScatterPlus (class in pypath.plot)
separate() (pypath.main.PyPath method)
separate_by_category() (pypath.main.PyPath method)
Seq (class in pypath.seq)
set_binary_data() (pypath.curl.Curl method), [1]
set_categories() (pypath.plot.MultiBarplot method)
set_chembl_mysql() (pypath.main.PyPath method)
set_colors() (pypath.plot.MultiBarplot method)
set_dir() (pypath.main.Direction method)
set_druggability() (pypath.main.PyPath method)
set_drugtargets() (pypath.main.PyPath method)
set_figsize() (pypath.plot.BarplotsGrid method)
(pypath.plot.CurationPlot method)
(pypath.plot.Dendrogram method)
(pypath.plot.HtpCharacteristics method)
(pypath.plot.MultiBarplot method)
(pypath.plot.RefsComposite method)
(pypath.plot.ScatterPlus method)
(pypath.plot.StackedBarplot method)
set_grid() (pypath.plot.BarplotsGrid method)
(pypath.plot.HtpCharacteristics method)
(pypath.plot.MultiBarplot method)
(pypath.plot.RefsComposite method)
set_kinases() (pypath.main.PyPath method)
set_progress() (pypath.pyreact.BioPaxReader method), [1]
set_receptors() (pypath.main.PyPath method)
set_signaling_proteins() (pypath.main.PyPath method)
set_title() (pypath.plot.BarplotsGrid method)
(pypath.plot.HtpCharacteristics method)
(pypath.plot.MultiBarplot method)
(pypath.plot.RefsComposite method)
(pypath.plot.ScatterPlus method)
(pypath.plot.StackedBarplot method)
set_transcription_factors() (pypath.main.PyPath method)
shortest_path_dist() (pypath.main.PyPath method)
signaling_proteins_list() (pypath.main.PyPath method)
signalink_interactions() (in module pypath.dataio)
signor_interactions() (in module pypath.dataio)
signor_urls() (in module pypath.dataio)
SimilarityGraph (class in pypath.plot)
sizes_edge() (pypath.plot.SimilarityGraph method)
small_plot() (pypath.main.PyPath method)
sort() (pypath.plot.MultiBarplot method)
source_network() (pypath.main.PyPath method)
src() (pypath.main.Direction method)
StackedBarplot (class in pypath.plot)
straight_between() (pypath.main.PyPath method)
sum_in_complex() (pypath.main.PyPath method)

T

take_a_trip() (in module pypath.dataio)
tfs_list() (pypath.main.PyPath method)
tgt() (pypath.main.Direction method)
third_source_directions() (pypath.main.PyPath method)
trembl_swissprot() (pypath.mapping.Mapper method)
trip_find_uniprot() (in module pypath.dataio)
trip_get_uniprot() (in module pypath.dataio)
trip_interactions() (in module pypath.dataio)
trip_process() (in module pypath.dataio)
trip_process_table() (in module pypath.dataio)

U

uniprot() (pypath.main.PyPath method)
UniprotMapping (class in pypath.input_formats)
uniprots() (pypath.main.PyPath method)
uniqList() (in module pypath.common)
unset_dir() (pypath.main.Direction method)
up() (pypath.main.PyPath method)
up_edge() (pypath.main.PyPath method)
update_cats() (pypath.main.PyPath method)
update_sources() (pypath.main.PyPath method)
update_vindex() (pypath.main.PyPath method)
update_vname() (pypath.main.PyPath method)
ups() (pypath.main.PyPath method)
url_fix() (pypath.curl.Curl method), [1]

V

values_to_sizes() (pypath.plot.ScatterPlus method)
vertex_pathways() (pypath.main.PyPath method)
vidal_hi_iii() (in module pypath.dataio)

W

which_table() (pypath.mapping.Mapper method)
Workflow (class in pypath.analysis)
write_tex() (pypath.plot.HistoryTree method)

Z

zenos_dichotomy() (in module pypath.colorgen)