I have 20 paired end libraries pseudomapped to the rat transcriptome with Salmon and I wish to create a tx2gene dataframe via the ensembldb package for downstream analysis in deseq2 as recommended here:
Note: if you are using an Ensembl transcriptome, the easiest way to create the
tx2gene data.frame is to use the ensembldb packages. The annotation packages can be found by version number, and use the pattern
transcripts function can be used with
return.type="DataFrame", in order to obtain something like the
df object constructed in the code chunk above. See the ensembldb package vignette for more details.
however, while biocLite("EnsDb.Hsapiens.v75") works fine, biocLite("EnsDb.Rnorvegicus.v89") returns: Warning message: package 'EnsDb.Rnorvegicus.v89' is not available (for R version 3.4.0)
Is this a case of trying to use the wrong tool, i.e these recommendations apply to human data but not other species... or some other issue? Would BioMart help?