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I want to know how to get orgDB to create KEGG pathway and GO analysis for soybean.
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You can check the AnnotationHub to see if there are any existing. Otherwise you can check out the AnnotationForge package for creating your own.
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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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