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SingleR-inc / SingleR

Clone of the Bioconductor repository for the SingleR package.
https://bioconductor.org/packages/devel/bioc/html/SingleR.html
GNU General Public License v3.0
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Tissue source of different reference data for single cell annotation #206

Closed amanzju closed 2 years ago

amanzju commented 2 years ago

Hi,

I'm trying to figure out the right reference data to annotate my own single-cell RNA-seq test data. Say, I have a test data of blood (PBMC) tissue from the human, and in this regard, if I'm not wrong, I can use the MonacoImmuneData reference dataset (since the corresponding GSE144434 dataset clearly mentioned that the PBMCs were isolate from human). For other reference datasets, I can't figure out tissue sources. Could you kindly explain to me how can I consider other reference datasets to annotate my own blood tissue sample dataset?

Thank you! Aman

j-andrews7 commented 2 years ago

See the celldex vignette for more information. Or check the documentation pages for each reference set, e.g. ?MonacoImmuneData.