Good morning to everyone,
To complete a DE genes analysis, at the end of my pipeline (during which I adopted DESEQ2 and edgeR methods, to compare results), I'd like to perform a GO enrichment analysis.
My main problem is that the GO terms aren't available on databases online, since I'm using a genome which is incomplete and only partially annotated. I'd like to use GO terms from that one.
I've tried to use the function goana from R, which I slightly changed to make it accept an external database, but it isn't working on my specific results, like I explained here.
I was considering topGo but it seems quite hard to adapt it to this purpose... I'd also be interested in something similar for KEGG analysis (for which I had thought of kegga from Bioconductor, but I guess I'm going to have similar issues).
Any suggestions there? What could I use which is free (I'm not going to buy BLAST2GO). Thanks in advance!