Annotation for S. pombe in gage.

Question

[Parham]

I am trying this workflow: "RNA-Seq Data Pathway and Gene-set Analysis Workflows Weijun Luo" but on S. pombe and not human data. In part 3.2 it starts with:

library(TxDb.Hsapiens.UCSC.hg19.knownGene)

I need help with finding the corresponding package for S. pombe instead of TxDb.Hsapiens.UCSC.hg19.knownGene

Cheers,
Parham

Answer 1

[Devon Ryan]

No such package exists. You can make your own TranscriptDB object with the GenomicFeatures package.

[Parham]

Thanks, I will try.

[Neilfws]

Just FYI the Bioconductor view for annotation packages is here and as Devon says, if it's not there, it doesn't exist. It is not too difficult to create something similar from UCSC genome data.