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Question: How to create gene set in cummerbund
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gravatar for icymoon
2.9 years ago by
icymoon • 0
United States
icymoon • 0 wrote:

There is tool to create gene set in cummerbund under R, how about under galaxy?
rna-seq galaxy • 1.2k views
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modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by icymoon • 0
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gravatar for Jennifer Hillman Jackson
2.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Please see the Galaxy NGS101 tutorial for how to manipulate the data: https://wiki.galaxyproject.org/Learn/GalaxyNGS101#Finding_differentially_expressed_transcripts

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you! But it seems there's no manipulation tutorial for cuffdiff sql output

ADD REPLY • link written 2.9 years ago by icymoon • 0

Did you watch the video? It has a demo for how to use some of the functions in Galaxy. The other functions are covered in the CummRbund manual (for data access/reduction). The output can also just be downloaded from Galaxy and used with the tool directly. Galaxy has RStudio available, and I see some tutorials for using that outside of Galaxy to perform certain additional functions (including the one your original question is about), but have not used it myself with this tool's data. (Found via a google, and we cannot recommend any but these are probably worth a look). 

This tool is very new to the public Main Galaxy instance. Some changes can be expected as usage increases, along with more documentation.

Others are still welcome to comment if they have more experience or advice to offer.

ADD REPLY • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k
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