pypath.inputs.msigdb.msigdb_download§

pypath.inputs.msigdb.msigdb_download(registered_email=None, collection='msigdb', id_type='symbols', force_download=False, organism='human', version=None)[source]§

Downloads and preprocesses a collection of gmt format gene sets from MSigDB. Returns dict of sets with gene set names as keys and molecular identifiers as values.

Parameters:

registered_email (str,NoneType) – An email address registered at MSigDB. If None the msigdb_email from pypath.settings will be used.
collection (str) – The name of the gene set collection. For available collections (e.g. h.all or c2.cpg) refer to the MSigDB website: http://software.broadinstitute.org/gsea/downloads.jsp#msigdb The default value msigdb contains all the genesets however you won’t be able to distinguish which geneset comes from which collection. For this you need to download the collections one by one.
id_type (str) – MSigDB provides Gene Symbols (symbols) and Entrez Gene IDs (entrez).
force_download (bool) – Download even if cache content is available.