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process_reactome

source 

.process_reactome(
   organism, infile = None, download_latest = False, filepath = None,
   omics_type = 'metabolomics', identifiers = None
)

Function to load Reactome pathways

Args

  • organism (str) : Reactome organism name
  • infile (str) : default None, provide a Reactome pathway file to process into the GMT-style dataframe
  • download_latest (Bool) : Downloads the latest version of Reactome metabolic pathways
  • filepath (str) : filepath to save pathway file to, default is None - save to variable
  • omics_type (str) : If using download_latest, specify type of omics pathways to download. Options are 'metabolomics', 'proteomics', 'transcriptomics', or 'multiomics'
  • identifiers (list) : list of identifiers to download for multi-omics pathways, default is None (download all). Options are 'chebi', 'uniprot', 'gene_symbol'

Returns

GMT-like pd.DataFrame containing Reactome pathways

process_kegg

source 

.process_kegg(
   organism, infile = None, download_latest = False, filepath = None,
   omics_type = 'metabolomics'
)

Function to load KEGG pathways

Args

  • organism (str) : KEGG organism code
  • infile (str) : default None, provide a KEGG pathway file to process into the GMT-style dataframe
  • download_latest (Bool) : Downloads the latest version of KEGG metabolic pathways
  • filepath (str) : filepath to save pathway file to, default is None - save to variable

Returns

GMT-like pd.DataFrame containing KEGG pathways

process_gmt

source 

.process_gmt(
   infile
)

Function to load pathways from a custom GMT-like file

Args

  • infile (str) : default None, provide a GMT pathway file to process into the GMT-style dataframe, file ending can be .csv or .gmt

Returns

GMT-like pd.DataFrame containing pathways

process_pathbank

source 

.process_pathbank(
   organism, infile = None, download_latest = False, filepath = None,
   omics_type = 'metabolomics'
)

Function to load PathBank pathways

Args

  • infile (str) : default None, provide a PathBank pathway file to process into the GMT-style dataframe
  • download_latest (Bool) : Downloads the latest version of PathBank metabolic pathways
  • filepath (str) : filepath to save pathway file to, default is None - save to variable
  • omics_type (str) : If using download_latest, specify type of omics pathways to download. Options are 'metabolomics', 'proteomics', or 'multiomics'

Returns

GMT-like pd.DataFrame containing PathBank pathways