Hi!
I was gene multiple files of gene expression matrix, each pertaining to an individual species. In each of the gene expression matrix, the row names are the genbank ID
For example, in a \
<Campylobacter jejuni> file, the rownames are: AHY39278, AHY39279... \
<Clostridioides difficile> file, the rownames are: CCL18761...
My questions is, is there any 'R' package that allows me to search for functional annotation based on these IDs? I am trying to add KEGG pathways, but if you have any other similar solutions (ie: GO), I don't mind giving it a go. I am mainly working from within 'R' so perhaps an R-based tool would be ideal.
Furthermore, its my first-time dealing with bacterial data. Therefore, if you could point me towards commonly used tools in analyzing bacteria genome, that'll be a great added bonus!
Thanks in advance!
Take a look at
GeneSCF(LINK). There are other programs in same category.