Looking for a package that compares my RNA seq data to find published dataset with a similar expression pattern
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@d27aed9d
Last seen 24 days ago
Germany

Hi,

is there a package out there that could take my RNA dataset (bulk or single cell) and compare it to published datasets to find those with the highest percentage of similarity to my dataset?

Thanks!

RNASeq • 191 views
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Sehyun Oh • 0
@6646b133
Last seen 15 days ago
United States

Hi! I think GenomicSuperSignature is what you are looking for.
This package matches new dataset to the public datasets through a gene expression pattern similarity.
It currently supports human bulk RNA-seq data with the planned expansions to different species/data types.
You can check more details in here:

Package: https://bioconductor.org/packages/release/bioc/html/GenomicSuperSignature.html
Use cases: https://shbrief.github.io/GenomicSuperSignaturePaper/
Preprint: https://www.biorxiv.org/content/10.1101/2021.05.26.445900v2

-Sehyun

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