GSVA R packages

Hello everyone,
I’m trying to do a gene set varian analysis using R to detect a specific gene set signature of a specific pathway from 20 samples of RNA-seq. I have this files in BAM format but I don’t know what to do in order to get a panel like this one in the pic!
which R packages are required?

on the Y axis there is the score for a specific singling pathway while the x axis represents the different samples.

Thank you

Hello,

Your best approach would be this:

1. produce a raw counts matrix for your BAM files (HT-seq,
   featureCounts, or something else)
2. normalise the raw counts (EdgeR, DESeq2, etc)
3. transform the normalised counts via, e.g., regularised log,
   variance stabilisation, or log2 (CPM + 1)
4. Run GSVA with the ‘C2’ Broad Institute curated datasets

The output of GSVA will be what you can then use to generate bar plot for each enriched signature / pathway.

I will leave the specifics of each step to you.

Kevin