Question

Fonction of genes/metabolites in a pathway?

0

Entering edit mode

emisecherre • 0

@emisecherre-23089

Last seen 4.3 years ago

Hello !

I'm looking for a tool (R or API if possible) which for a given pathway return genes and/or metabolites involved in it and their function in the pathway.

Thanks in advance for your help !

gene metabolite functionnal annotation pathways • 1.2k views

ADD COMMENT • link updated 4.7 years ago by Kevin Blighe ★ 4.0k • written 4.7 years ago by emisecherre • 0

score 0 · Answer 1 · 2020-03-25

0

Entering edit mode

Kevin Blighe ★ 4.0k

@kevin

Last seen 29 days ago

Republic of Ireland

If you are working with Metabolomics data, then you at least need to be aware of MetaboAnalyst, which has an associated R package and API.

However, be aware that the R package, MetaboAnalystR, is not on Bioconductor.

Kevin

ADD COMMENT • link 4.7 years ago Kevin Blighe ★ 4.0k

0

Entering edit mode

I'm awared of it already, the thing is that i couldn't install it even with dev help...

ADD REPLY • link 4.7 years ago emisecherre • 0

0

Entering edit mode

Please elaborate on the errors that you faced.

ADD REPLY • link 4.7 years ago Kevin Blighe ★ 4.0k

0

Entering edit mode

It's when i tried to do this step of a pipeline (checked by the dev) :

> mSet<-PerformIntegCmpdMapping(mSet, cmpdList, "hsa", "kegg");

[1] "Reading data unsuccessful, attempting to re-download file..." % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 497k 100 497k 0 0 463k 0 0:00:01 0:00:01 --:--:-- 463k [1] "Loading files from server unsuccessful. Ensure curl is downloaded on your computer." Error in .read.metaboanalyst.lib("compound_db.rds") : objet 'my.lib' introuvable

ADD REPLY • link 4.7 years ago emisecherre • 0