How to perform deconvolution with RPKM values

xuranw / MuSiC

Multi-subject Single Cell Deconvolution

https://github.com/xuranw/MuSiC

GNU General Public License v3.0

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How to perform deconvolution with RPKM values #34

Open chenming9453 opened 4 years ago

chenming9453 commented 4 years ago

Hi Xuran,

I tried to apply MuSiC to RNAseq bulk data with RPKM as the input. According to your paper(Discussion), "MuSiC can utilize RPKM if estimates of cell type-specific total RNA abundance can be provided." I am wondering how I can incorporate cell-type-specific total RNA abundance into your function? Or can I directly use RPKM as the input and use music_prop to do the deconvolution? Does my reference single-cell RNAseq data also requires RPKM as the input? Thanks!

Best, Ming

zhanglab2008 commented 3 years ago

I brought up this thread since I also have the same question. A lot of people only make RPKM count matrices available to download from GEO so it will be hugely helpful if the MuSiC author can provide a way to analyze the RPKM file. Many thanks!