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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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Possible to merge multiple single cell datasets to create a reference compatible with MuSiC? #122

Open CaitlinGHowe opened 11 months ago

CaitlinGHowe commented 11 months ago

I'm curious if anyone knows how to appropriately merge multiple single cell datasets to create a reference dataset that's compatible with MuSiC? I'm trying to deconvolute a bulk RNA-seq dataset from buffy coat, so I need a single cell reference that includes neutrophils in addition to PBMCs. I'm trying to create this reference using multiple datasets. However, all of the methods that I've come across for merging multiple single cell datasets require that the data be normalized. Given that MuSiC requires raw counts as the input I'm not clear how to best merge multiple single cell datasets in a way that generates a dataset compatible with MuSiC. Any suggestions or thoughts on this would be very appreciated. Thanks!

adomingues commented 10 months ago

I came to ask the exact same question @CaitlinGHowe!

youcef-benmohammed commented 3 months ago

Hello, I'm currently tackling a similar challenge, I'm dealing with multiple single-cell datasets, have you tried data integration before you run deconvolution?