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samuel-marsh / scCustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
https://samuel-marsh.github.io/scCustomize/
GNU General Public License v3.0
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Additional features to implement #95

Closed kasumaz closed 1 year ago

kasumaz commented 1 year ago

Hi, Just an idea: I use seurat (and now also sc customize) and sometimes also DESEQ2 for bulk experiments. I often have to find time to connect the gene lists that come out of a differential expression analysis to additional tools like clusterprofiler to then do some pathway/GO analysis. It would be handy to be able to do this without setting up further code and maybe even store this information within seurat/DESEQ2 objects. Thanks.

samuel-marsh commented 1 year ago

Hi,

Can you better explain what you mean by connect the gene lists? What are you thinking new function would do specifically?

thanks! Sam

kasumaz commented 1 year ago

What I mean, if there was a way to perform gene ontology/pathway analysis right from the gene lists produced. I could do this myself via using clusterprofiler, but others may not be able to. This sort of follow-up analysis is always missing from single cell analysis tools.

samuel-marsh commented 1 year ago

Hi @kasumaz

Sorry for delay here, it's been very busy spring. I think I'm going to hold on this for now as I'm not sure I have time to get into this for a bit. If you have idea and want to submit PR I'd be happy to take a look.

Best! Sam