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lanagarmire / Granatum

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Feature: Let users add new References #1

Open subwaystation opened 6 years ago

subwaystation commented 6 years ago

Hi there, I would like to add a new genome reference to use with Granatum. This is not possible, yet? Best, Simon

lanagarmire commented 6 years ago

That is a good idea. Yes, we should consider it. Perhaps we need to encourage user upload of genome interpretation of their preference.

What do you think, team?

On Nov 9, 2017 5:22 AM, "Simon Heumos" notifications@github.com wrote:

Hi there, I would like to add a new genome reference to use with Granatum. This is not possible, yet? Best, Simon

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lanagarmire commented 6 years ago

Yes I agree. So by genome reference you mean as opposed to RefSeq?

On Nov 9, 2017 6:01 AM, "Lana Garmire" lgarmire@gmail.com wrote:

That is a good idea. Yes, we should consider it. Perhaps we need to encourage user upload of genome interpretation of their preference.

What do you think, team?

On Nov 9, 2017 5:22 AM, "Simon Heumos" notifications@github.com wrote:

Hi there, I would like to add a new genome reference to use with Granatum. This is not possible, yet? Best, Simon

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/lanagarmire/Granatum/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AIpGOywg6s_RTecn0Y_MWwR6pR1nyzGaks5s0xizgaJpZM4QYIm0 .

subwaystation commented 6 years ago

At the moment you provide Human and Mouse. And I would be able to add another organism? Would that be hard to implement?

lanagarmire commented 6 years ago

One place that the reference genome is a must is gene set enrichment. Other steps should be mostly fine. It may be tricky to do KEGG analysis in other organisms, the user may need to be provide the physical mapping between genes and pathway IDs.

On Nov 9, 2017 10:22 PM, "Simon Heumos" notifications@github.com wrote:

At the moment you provide Human and Mouse. And I would be able to add another organism? Would that be hard to implement?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lanagarmire/Granatum/issues/1#issuecomment-343407026, or mute the thread https://github.com/notifications/unsubscribe-auth/AIpGO69M_Br90CsCzB7lIxcRPREETUjyks5s1AfhgaJpZM4QYIm0 .