Brachypodium distachyon db
1
@a75c4c91
Last seen 8 months 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
• 330 views
@james-w-macdonald-5106
Last seen 6 hours 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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loading from cache
Then go from there.
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