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input pathway database directory #5

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BhaktiDwivedi opened this issue Apr 2, 2019 · 0 comments
Open

input pathway database directory #5

BhaktiDwivedi opened this issue Apr 2, 2019 · 0 comments

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@BhaktiDwivedi
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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.

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