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I want to know how to get orgDB to create KEGG pathway and GO analysis for soybean.
I want to know how to get orgDB to create KEGG pathway and GO analysis for soybean.
You can check the AnnotationHub to see if there are any existing. Otherwise you can check out the AnnotationForge package for creating your own.
You should look at the documentation on the help pages for those packages. It should be clear enough there. But to speed things along:
> library(AnnotationHub)
> ah = AnnotationHub()
> query(ah, c("Glycine", "max"))
AnnotationHub with 11 records
# snapshotDate(): 2025-03-03
# $dataprovider: NCBI,DBCLS, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, Inparanoid8
# $species: Glycine max, Glycine max_subsp._soja
# $rdataclass: SQLiteFile, OrgDb, Inparanoid8Db
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH10511"]]'
title
AH10511 | hom.Glycine_max.inp8.sqlite
AH91607 | MeSHDb for Glycine max (Soybean, v001)
AH97874 | MeSHDb for Glycine max (Soybean, v002)
AH100339 | MeSHDb for Glycine max (Soybean, v003)
AH107104 | MeSHDb for Glycine max (Soybean, v004)
... ...
AH114015 | MeSHDb for Glycine max (Soybean, v006)
AH116642 | MeSHDb for Glycine max (Soybean, v007)
AH117133 | MeSHDb for Glycine max (Soybean, v008)
AH117368 | org.Glycine_max_subsp._soja.eg.sqlite
AH117372 | org.Glycine_max.eg.sqlite
So it does look like its available in the hubs. I will allow you to look at the documentation to find out how to download
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Thanks for the suggestion! I'll check out the resources.