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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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PIN and custom genes specific to Mice #13

Closed Manti19 closed 5 years ago

Manti19 commented 5 years ago

I am working with mice data. It seems pathfindR package works with human data. How can the define PIN to Mice specific and custom genes too.

egeulgen commented 5 years ago

You may follow the instructions provided here on issue #5 With this you can provide a custom gene list (which you will have to find) and a custom PIN (which you will have to find) and run pathfindR to obtain mouse pathways.

In the tutorial on biostars you may find a more detailed version of the instructions (under pathfindR Analysis with Custom Gene Sets).

Hope this helps,

egeulgen commented 5 years ago

vignette for non-human organisms

Manti19 commented 5 years ago

I am not able to access it..

On Sun, Jun 2, 2019 at 8:32 PM Ege Ulgen notifications@github.com wrote:

https://camo.githubusercontent.com/193766a3b9959c5f4ed5cd8cf3251d015e839d51/68747470733a2f2f6769746875622e7472656c6c6f2e73657276696365732f696d616765732f6d696e692d7472656c6c6f2d69636f6e2e706e67 vignette for non-human organisms https://trello.com/c/l2HbHr4y/73-vignette-for-non-human-organisms

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/egeulgen/pathfindR/issues/13?email_source=notifications&email_token=ALBKCGKCL2ANABNK6NI4J4DPYPOGZA5CNFSM4GUMCT72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWXXP6I#issuecomment-498038777, or mute the thread https://github.com/notifications/unsubscribe-auth/ALBKCGJMP6PMORYVYZP6Y23PYPOGZANCNFSM4GUMCT7Q .

-- Regards, Manti

egeulgen commented 5 years ago

That is only an auto-comment to indicate that a task regarding this issue was created (our team’s private Trello board). I’ll provide an update once the planned vignette is created.