[Bioc-devel] OrgDB entry for Homo sapiens and Mus musculus missing in AnnotationHub

[Kern, Lori]

We apologize for the disruption. They have been reinstated and should now be available.



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 using r-project.org> on behalf of Alex Wong <alexchwong.github using gmail.com>
Sent: Saturday, October 12, 2024 7:49 PM
To: bioc-devel using r-project.org <bioc-devel using 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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