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xuranw / MuSiC

Multi-subject Single Cell Deconvolution
https://github.com/xuranw/MuSiC
GNU General Public License v3.0
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How to handle TCGA RNAseq data? #115

Open apxmfrstmc opened 1 year ago

apxmfrstmc commented 1 year ago

If I want to analyze the RNAseq data of TCGA, which data should be used? count or tpm or fpkm?

jebard commented 1 year ago

Helpful reference that explores normalizations and the effects on deconvolution -- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7648640/

ChiaraCaprioli commented 1 year ago

And here an update https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03016-6