Fonction of genes/metabolites in a pathway?
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@emisecherre-23089
Last seen 13 months 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 • 216 views
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@kevin
Last seen 14 minutes 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

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

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Please elaborate on the errors that you faced.

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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

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