Genes in enriched pathways

[ziyan109]

Hello,

This is such a great tool and I was able to generate the heatmap :)
I'm wondering is there any function to pull out the genes that are enriched in certain pathway? For example, TGF-beta signaling pathway is enriched in one of my clusters, I wonder which genes are up-regulated in there.

Thanks so much.

[arc85]

Hi Ziyan, great point. It would be helpful to explore "leading edge" genes directly from this package.

[abedkurdi]

Excuse me, but where to find the function related to "leading edge"?

[ziyan109]

Hi, I was referring to the "leading edge gene" returned by the fgsea package. Is it possible to do it in singleseqgset? Thanks!

…

On Thu, Jan 5, 2023 at 11:15 AM Abdullah El Kurdi ***@***.***> wrote: Excuse me, but where to find the function related to "leading edge"? — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/arc85/singleseqgset/issues/2*issuecomment-1372628098__;Iw!!Mih3wA!CjnGPtP1MzvCmPRiwiMnrDlY7zqg79GHknh5iGc4oGJpHMIKLAtYucH27c1jVmhGzrPxhyLQPm5bWMFYB58mujPJLRE$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AH7ZA2YBTYTGKSF2MQUSPNDWQ4MWJANCNFSM4NZBQI2A__;!!Mih3wA!CjnGPtP1MzvCmPRiwiMnrDlY7zqg79GHknh5iGc4oGJpHMIKLAtYucH27c1jVmhGzrPxhyLQPm5bWMFYB58mtqK1WF8$> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[abedkurdi]

Yeah, I guess, but no idea how. I will give it a try when I have some time.