I am working with several E. coli samples, for each of which I have a list of hundreds of differentially expressed genes deriving from DESeq2. Besides log 2 fold change and p-value, I also have their expression in TPM and FPKM. I also have the annotated GO terms for each gene.
With all these data I would like to perform a gene set enrichment analysis, once for each sample. Hence, I would need something that works from command line and that accepts E. coli gene names. I would much prefer if the expression levels could be used to rank genes.
The tools I know are:
I am basically a neophyte with all these tools. I know that some of them are mostly made for human or mice datasets, and some other (DAVID) are debatable in terms of reliability.
All the posts I found on BioStars about this are either not centred on E. coli or quite old (4-5 years ago). Hence, what way would you suggest me to proceed?