Question

How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?

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mathavanbioinfo ▴ 20

@mathavanbioinfo-11955

Last seen 7 months ago

India

Dear All, I am working on whole transcriptome analysis on Oryza sativa Japonica and Oryza sativa Indica, I want to proceed with the pathway analysis using the ReactomePA package. Please guide me on where to download the annotation package for the species mentioned above.

For example I used these packages for pathway analysis for human library(ReactomePA) library(clusterProfiler) library(org.Hs.eg.db)

reactomePA package annotation • 1.6k views

ADD COMMENT • link updated 2.8 years ago by shepherl 4.1k • written 2.8 years ago by mathavanbioinfo ▴ 20

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For Oryza sativa Japonica, It looks like there might be an option in AnnotationHub. But there doesn't appear to be an option in AnnotationHub yet for Oryza sativa Indica

> ah = AnnotationHub::AnnotationHub()
snapshotDate(): 2022-01-07
> AnnotationHub::query(ah, c("Oryza", "Japonica"))
AnnotationHub with 5 records
# snapshotDate(): 2022-01-07
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, NCBI,DBCLS
# $species: Oryza sativa Japonica Group, Oryza sativa_subsp._japonica, Oryza...
# $rdataclass: OrgDb, SQLiteFile
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH91623"]]' 

            title                                               
  AH91623 | MeSHDb for Oryza sativa Japonica Group (Rice, v001) 
  AH96211 | org.Oryza_sativa_(japonica_cultivar-group).eg.sqlite
  AH96212 | org.Oryza_sativa_Japonica_Group.eg.sqlite           
  AH96213 | org.Oryza_sativa_subsp._japonica.eg.sqlite          
  AH97890 | MeSHDb for Oryza sativa Japonica Group (Rice, v002) 
> query(ah, c("Oryza", "Indica"))
AnnotationHub with 0 records
# snapshotDate(): 2022-01-07

ADD REPLY • link 2.8 years ago shepherl 4.1k