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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
MIT License
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Diffbind with EdgeR #2327

Open alexlenail opened 5 years ago

alexlenail commented 5 years ago

The galaxy Diffbind tool doesn't seem to have an option to use EdgeR instead of DESeq2 underneath. The galaxy Diffbind tool markdown says:

it uses statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages edgeR and DESeq2)

the core analysis routines are executed, by default using DESeq2

But the option to use EdgeR is not surfaced. From the Diffbind docs (section 7.4):

When dba.analyze is invoked using the default method=DBA_EDGER, a standardized differential analysis is performed using the edgeR package.

That should be an option passed to this line:

https://github.com/galaxyproject/tools-iuc/blob/a0c51ab52c4e3f296d5577ee3af26c4c1465e1e9/tools/diffbind/diffbind.R#L81

mblue9 commented 5 years ago

Hi @zfrenchee yes, that is noted here: https://github.com/galaxyproject/tools-iuc/issues/1809#issue-311041264 PR welcome!