pypath.inputs.msigdb.msigdb_download_collections§

pypath.inputs.msigdb.msigdb_download_collections(registered_email=None, only_collections=None, exclude=('c5', 'm5'), id_type='symbols', organism='human', version=None)[source]§

Downloads all or some MSigDB gene set collections. Returns a dict of dicts where upper level keys are collections while lower level keys are geneset names and values are molecular identifiers.

Parameters:

registered_email (str,NoneType) – An email address registered at MSigDB. If None the msigdb_email from pypath.settings will be used.
only_collections (set,NoneType) – Limit the annotations only to these collections. For available collections e.g. {'h.all', 'c2.cgp'} refer to the MSigDB webpage: http://software.broadinstitute.org/gsea/downloads.jsp#msigdb
exclude (tuple) – Exclude the collections having their name starting with any of the strings in this tuple. By default c5 and m5 (Gene Ontology and Human/Mouse Phenotype Ontology) is excluded.