Question: Annotation for S. pombe in gage.
0
gravatar for Parham
6.3 years ago by
Parham1.5k
Sweden
Parham1.5k wrote:

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

gage s. pombe • 1.4k views
ADD COMMENTlink modified 6.3 years ago by Devon Ryan96k • written 6.3 years ago by Parham1.5k
1
gravatar for Devon Ryan
6.3 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

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

ADD COMMENTlink written 6.3 years ago by Devon Ryan96k

Thanks, I will try.

ADD REPLYlink written 6.3 years ago by Parham1.5k
1

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.

ADD REPLYlink modified 8 months ago by RamRS30k • written 6.3 years ago by Neilfws48k
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