input pathway database directory #5
Description
Hi,
I am interested in running ipanda to identify activated pathways among the differentially expressed genes from RNA-seq data. I would like to use Kegg, Reactome, NCI, Biocarta, PPI input pathway databases. Are these databases directory available via ipanda?
For example, in the 'sample_kegg' folder that comes with the package, I can generate, gene_list.txt, pathway_list.txt, pathway_contents.txt for my own pathway databases; however, I am not sure how to obtain modules.txt, pathway_akk.txt, and gene module information in pathway_contents.txt. Is there an automated way to compute these additional calculations and generate these files for custom pathway databases?
Appreciate your help and any suggestions. Thank you.