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Annotation for S. pombe in gage.

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

s.pombe gage
• 3,376 views • link
updated by Ram Ram • written by Parham Parham

1 answer

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

• 2 views • link
written by Devon Ryan Devon Ryan

Thanks, I will try.

• 2 views • link
written by Parham Parham

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.

• 0 views • link
updated by Ram Ram • written by Neilfws Neilfws

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