Major changes

  • Added the gene_sets option in run_pathfindR to chose between different gene sets. Available gene sets are KEGG, Reactome, BioCarta and Gene Ontology gene sets (GO-BP, GO-CC and GO-MF)
  • cluster_pathways automatically recognizes the ID type and chooses the gene sets accordingly

Minor changes and bug fixes

  • Fixed issue regarding p values < 1e-13. No active subnetworks were found when there were p values < 1e-13. These are now changed to 1e-13 in the function input_processing
  • In input_processing, genes for which no interactions are found in the PIN are now removed before active subnetwork search
  • Duplicated gene symbols no longer raise an error. If there are duplicated symbols, the lowest p value is chosen for each gene symbol in the function input_processing
  • To prevent the formation of nested folders, by default and on errors, the function run_pathfindR returns to the user’s working directory.
  • Citation information are now provided for our BioRxiv pre-print