Question: Getting Figures from R with Galaxy DESEQ2 output?
gravatar for amaheras7091
17 months ago by
amaheras709110 wrote:


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



ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson24k • written 17 months ago by amaheras709110
gravatar for y.hoogstrate
17 months ago by
y.hoogstrate460 wrote:

Dear amaheras7091,


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.


ADD COMMENTlink written 17 months ago by y.hoogstrate460

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 I shall create a github accordingly. Thank you for your assistance.

ADD REPLYlink written 17 months ago by amaheras709110
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 64 users visited in the last hour