Question

Annotation package for Manduca sexta

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@293af73d

Last seen 3 days ago

United States

Hello, Does Bioconductor have an annotation package like org.Dm.eg.db but for Manduca sexta?

Thank you for your help.

annotation Manducasexta AnnotationData • 333 views

ADD COMMENT • link 5 days ago • updated 3 days ago GA ▴ 10

score 0 · Answer 1 · 2025-03-25

Yes through the AnnotationHub

> library(AnnotationHub)

> ah = AnnotationHub()
snapshotDate(): 2024-10-28

> query(ah, "Manduca")
AnnotationHub with 1 record
# snapshotDate(): 2024-10-28
# names(): AH118702
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Manduca sexta
# $rdataclass: OrgDb
# $rdatadateadded: 2024-10-04
# $title: org.Manduca_sexta.eg.sqlite
# $description: NCBI gene ID based annotations about Manduca sexta
# $taxonomyid: 7130
# $genome: NCBI genomes
# $sourcetype: NCBI/UniProt
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.uniprot.org/p...
# $sourcesize: NA
# $tags: c("NCBI", "Gene", "Annotation") 
# retrieve record with 'object[["AH118702"]]' 

org <- ah[["AH118702"]]

If there is ever one that is not available the code to construct your own can be found in the AnnotationForge package.