incomplete C8 download with msigdbr

[Anton Gluck]

There seems to be an issue when downloading the C8 gene set collection with msigdbr: as per MSigDB website, C8 has 830 gene sets - but when downloading it there are only 700 gene sets.

Any suggestions about how this could be fixed?

[Anthony Castanza]

Hi Anton,

MSigDBR is not a piece of software we produce, it's a 3rd party package that redistributes MSigDB, I'd recommend reaching out to them directly using whatever email address they provide in the support information for the package. That said the issue here might be that it's bundling an old version of MSigDB. The current version is always available from our MSigDB.org website and these sorts of packages typically have a way to load in our gmt files directly.

Sorry I couldn't be of more help here

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

On Tue, Jun 25, 2024, 6:05 AM Anton Gluck <acmg...@gmail.com> wrote:

There seems to be an issue when downloading the C8 gene set collection with msigdbr: as per MSigDB website, C8 has 830 gene sets - but when downloading it there are only 700 gene sets.

Any suggestions about how this could be fixed?

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[Anton Gluck]

Hi Anthony,

Thank you for your reply, this is already quite helpful. As you suggest, I will reach out to the msigdbr R package authors.

Best regards,

Anton