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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.
The text was updated successfully, but these errors were encountered:
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.
The text was updated successfully, but these errors were encountered: