hallmark_genesets.gmt

[Ruzong Fan]

Dear Sir/Madam,

In the paper of 

Cable et al. (2022). Cell type-specific inference of differential expression in spatial transcriptomics. Nature Methods, 19, 1076-1087

 it uses a dataset named 

hallmark_genesets.gmt

from you. But I can not find it. 

I wonder if you may help?

[Anthony Castanza]

Hello,

All of our gmt files from recent MSigDB released are versioned with information about which specific release they were retrieved from. Without information from the authors of this paper on which version they retrieved their data from its impossible to say what database version they used.

They do say that it was Hallmark data from MSigDB, so our current Hallmarks collection would be the current equivalent, but if you need the exact version match, I would suggest checking the supplementary data to see if it is disclosed there. If not, you would likely need to reach out to the authors of that manuscript.

Sorry I couldn't be of more assistance

-Anthony

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

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