Hi all,

I have a question regarding UCSC Genome. I have gone through the process of using galaxy (tophat, cuff diff, etc) and I used the mouse Dec2011 mm10 as my annotation file. What I currently have are all the NM_#### and NR_#### for the genes, but I need the gene names. I was able to get a .csv that had quite a few, so I just used R to search (grep) and match the names for me, but the file does not have all of them.

So I have installed the TxDb.Mmusculus.UCSC.mm10.knownGene package, but can't figure out how to do this very simple task. I'm hoping there is a function that allows me to input, for example, NM_001001130, and the gene name Zfp85 would be returned.

Thank you in advance for you time and expertise!

You want the org.Mm.eg.db package, and you should read the help page for select().

> library(org.Mm.eg.db)
Loading required package: AnnotationDbi
Loading required package: GenomeInfoDb

> select(org.Mm.eg.db, "NM_001001130", "SYMBOL","REFSEQ")
        REFSEQ SYMBOL
1 NM_001001130  Zfp85