Brachypodium distachyon db
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Leyre • 0
@a75c4c91
Last seen 12 days ago
Spain

Hello I am traying to anlalised a Brachypodium dystachion analysis . Could someone help me . Whe using arabidopsisi is easier because there is the package for it how can I us a code like this if there is no package for Brachypodium. Can I create and object with a link to the enable plants brachy genome or which data I should download. Is possible to create a pakcege for a grass model plant as brachypoidum dystachion? Thanks for your time and your help.


 enrichGO(gene = de_genes,
                universe = all_genes,
                keyType = "ENTREZID",
                OrgDb = org.At.tair.db, # adapt to brachypodium distachion
                ont = "BP",
                pAdjustMethod = "BH",
                qvalueCutoff = 0.05,
                readable = TRUE)
EnrichmentBrowser BrachypodiumDB RNASeqData • 83 views
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@james-w-macdonald-5106
Last seen 3 days ago
United States
> library(AnnotationHub)
> hub <- AnnotationHub()
snapshotDate(): 2023-10-23
> query(hub, c("orgdb","brachypodium"))
AnnotationHub with 1 record
# snapshotDate(): 2023-10-23
# names(): AH114855
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Brachypodium distachyon
# $rdataclass: OrgDb
# $rdatadateadded: 2023-10-20
# $title: org.Brachypodium_distachyon.eg.sqlite
# $description: NCBI gene ID based annotations about Brachypodium distachyon
# $taxonomyid: 15368
# $genome: NCBI genomes
# $sourcetype: NCBI/UniProt
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.uniprot.org/pub/databases/uniprot/current_releas...
# $sourcesize: NA
# $tags: c("NCBI", "Gene", "Annotation") 
# retrieve record with 'object[["AH114855"]]' 
> org.Bp.eg.db <- hub[["AH114855"]]
downloading 1 resources
retrieving 1 resource
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