orgDB
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Fatima • 0
@036d2727
Last seen 6 days ago
South Korea

I want to know how to get orgDB to create KEGG pathway and GO analysis for soybean.

IlluminaDataTestFiles • 352 views
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Thanks for the suggestion! I'll check out the resources.

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shepherl 4.1k
@lshep
Last seen 6 hours ago
United States

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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how to do that?

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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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