Question: Help For Usage Of Gene2Pathways(R Package For Kegg)
gravatar for Casual
7.1 years ago by
Casual90 wrote:

Hi~ I have batch of differentially expressed genes/transcripts ID & sequence from A Non-Model organism. I wanted to align these genes/transcripts to KEGG pathways to find the most possible pathways being triggered. After some searching work, I got the gene2pathways package might do this job~ But I read it's manual, too brief for me,such a R beginner :( Could anybody show me how to use this package,or even better, suggest another soft suit? By the way, my organism is not in the kegg supported species list yet.So it's still possible to get the pathway information, isn't it?

The reference I used was torafugu(fish), the Ensembl ID were like " ENSTRUT00000000001 ENSTRUP00000000001 ENSTRUG00000000001" ,actually it's not my real specie,only the most closely related one~

R non kegg • 2.5k views
ADD COMMENTlink modified 5.6 years ago by Biostar ♦♦ 20 • written 7.1 years ago by Casual90

You can most likely not use this package, because it appears to be only working for flybase identifiers (or KEGG is broken). Even some examples don't work (tried 'retrain' to get a model for "hsa", or "dfru" the kegg organism code for fugu). I'd nag the authors if you really need it.

ADD REPLYlink written 7.1 years ago by Michael Dondrup46k

Why the output format is so wired? It's fine when I was typing~

ADD REPLYlink written 7.1 years ago by Casual90

Can you tell us which organism you are working with and provide some sample gene/transcript ids (edit your question to include these details)? If you are lucky someone will help to walk you through this.

ADD REPLYlink written 7.1 years ago by Obi Griffith17k

Michael,Sorry I didn't quite follow U.What's your recommendation?A new package?or...?

ADD REPLYlink written 7.1 years ago by Casual90
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