Pathway enrichment and analysis of mice gene sets in R platform

Question

[slg.manti]

I am working on RNA-Seq data of mice samples. Is there a R package for pathway(KEGG,Biocarta) enrichment and analysis for mice specific genesets?

[Benn]

Yes there are, what have you tried?

[slg.manti]

I tried pathfindR . But it is not working due to default Human setup.

[Benn]

If you want to stick to pathfindR, you can use a custom dataset which you can get from biomaRt. I haven't tried it, but this describes how to do it.

Another option is to use GOseq, you can use KEGG and REACTOME datasets as well (I think there is a example in the manual with KEGG data).

[slg.manti]

I got the custom genesets and custom pathways mice specific using KEGGREST package. I also need Protein-protein interaction network path mice specific. Is there any package for that?

[Benn]

Most popular ppi database is string, there is an R package called STRINGdb, but I am not sure if you can use that similar as the genesets/pathways.

[Buffo]

I recommend you to use webgestalt, personally I think it works even better and easier than R packages.

Answer 1

[caggtaagtat]

Hi, I like the EGESA package, which combines a set of already existing tools, into one output.