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?
Yes there are, what have you tried?
I tried pathfindR . But it is not working due to default Human setup.
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).
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?
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.
I recommend you to use webgestalt, personally I think it works even better and easier than R packages.
Hi, I like the EGESA package, which combines a set of already existing tools, into one output.