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Question: Getting Figures from R with Galaxy DESEQ2 output?
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gravatar for amaheras7091
2.2 years ago by
amaheras7091 • 10
amaheras7091 • 10 wrote:

Hi,

So this summer I ran a bioinformatics workflow on differential gene expression in three samples in galaxy (shown below) and now I want to use R to get publishable figures. If I have the DESeq2 results output, is there a way to view and manipulate these tabular files on R and create graphs/figures (eg. heat maps). Or does anyone have a program they could recommend that would could also produce publishable figures from my DESeq2 output?

Galaxy: FastQC FastQGroomer FastQ Quality Trim Trim Galore! TopHat BAM to SAM Ht-seq count DESeq2

Thanks,

Amanda

rna-seq figures graphs statistics publication • 853 views
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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by amaheras7091 • 10
1
gravatar for y.hoogstrate
2.2 years ago by
y.hoogstrate • 460
Netherlands
y.hoogstrate • 460 wrote:

Dear amaheras7091,

https://github.com/galaxyproject/tools-iuc/pull/20#issuecomment-137977082

"

A feature request that I got for a similar tool is an opt-in option to export the RData object so people can continue with it in their own R instance (or Galaxy RStudio).

...

Ah, yes, makes sense. Can we add this in a later version, I really would like to get this release out. I have promised so many people a proper DESeq2 release since month :)

"

It was part of the plan, but I think we lost track of it.. If it's really important to you, feel free to create a github issue. I am willing to work on this but I don't have too much time for this.

Youri
ADD COMMENT • link written 2.2 years ago by y.hoogstrate • 460
1

I discussed the issue with my research advisor, and we both agree that such a feature would be incredibly beneficial for our intentions to publish with our data we have thus far analyzed through use galaxy.com. I shall create a github accordingly. Thank you for your assistance.

ADD REPLY • link written 2.2 years ago by amaheras7091 • 10
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