[Bioc-devel] OrgDB entry for Homo sapiens and Mus musculus missing in AnnotationHub
Thank you for letting us know. We will investigate the issue. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Alex Wong <alexchwong.github at gmail.com>
Sent: Saturday, October 12, 2024 7:49 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] OrgDB entry for Homo sapiens and Mus musculus missing in AnnotationHub
Sent: Saturday, October 12, 2024 7:49 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] OrgDB entry for Homo sapiens and Mus musculus missing in AnnotationHub
Hi there,
It seems that OrgDB entries for human and mouse have recently been removed
from AnnotationHub for Bioc 3.19, then re-entered into Bioc devel. This
database change breaks (my package) SpliceWiz for Bioc 3.19 but continues
to work for Bioc devel.
Reprex: the following returns `TRUE` for Bioc devel but `FALSE` in Bioc
3.19:
'''
library(AnnotationHub)
ah <- AnnotationHub()
ah_orgList <- subset(ah, ah$rdataclass == "OrgDb")
supportedSpecies <- unique(ah_orgList$species)
any(supportedSpecies == "Homo sapiens")
'''
Kind Regards,
Alex Wong
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