Differential expression analysis with limma-voom

Question: Differential expression analysis with limma-voom

9 days ago by

fraheto • 10 wrote:

Hi there: I have been following your tutorial "RNA-Seq reads to counts" https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/limma-voom_fastqs_to_counts/tutorial.html I have found it very useful. It seems to be the first part of a more complet RNA-seq workflow. In this tutorial you indicate that "Differential expression analysis with limma-voom is covered in an accompanying tutorial". However I can not find this second part. Please, could you be so kind to show me where is this second part? I have been looking for it but I could not find it. Regards

rna-seq limma • 63 views

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modified 2 days ago by mblue9 • 140 • written 9 days ago by fraheto • 10

4 days ago by

mblue9 • 140

mblue9 • 140 wrote:

Hello, great to hear that you found it useful! (and cool that you found it all, it's a hidden tutorial at the moment :)) I haven't quite finished the 2nd tutorial, I'm going to break that one into 2 (make a separate tutorial for the gene set testing), as it's quite long, but here it is: https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/limma-voom/tutorial.html

ADD COMMENT • link written 4 days ago by mblue9 • 140

Thank you for such a nice contribution. Your tutorials are awesome. I have been following the second part, but I am stuck in the beginning. I can not find the tool annotateMyIDs in the tool panel. It seems that it has not been added to it, right? Could you help me with this issue? Thank you very much.

ADD REPLY • link written 3 days ago by fraheto • 10

Hello,

The tool annotateMyIDs is currently installed at the Galaxy EU public server https://usegalaxy.eu and available in the ToolShed https://usegalaxy.org/toolshed for a local/cloud/docker Galaxy servers.

There are plans to install it at Galaxy Main https://usegalaxy.org near-term. Tracking ticket: https://github.com/galaxyproject/usegalaxy-playbook/issues/141

Thanks! Jen, Galaxy team

ADD REPLY • link written 3 days ago by Jennifer Hillman Jackson ♦ 25k

Hi fraheto, thanks for the nice words! :)

Just to add to what Jen said, the whole tutorial should run at https://usegalaxy.eu, all the required tools should be installed there.

ADD REPLY • link written 2 days ago by mblue9 • 140

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