Multi-subject Single Cell deconvolution (MuSiC)

MuSiC is a deconvolution method that utilizes cross-subject scRNA-seq to estimate cell type proportions in bulk RNA-seq data.

How to cite MuSiC

Please cite the following publication:

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference
X. Wang, J. Park, K. Susztak, N.R. Zhang, M. Li
Nature Communications. 2019 Jan 22 https://doi.org/10.1038/s41467-018-08023-x

Installation

# install devtools if necessary
install.packages('devtools')

# install the MuSiC package
devtools::install_github('xuranw/MuSiC')

# load
library(MuSiC)

More Information

Please see Tutorial.

Note of the current repository

This repository is a fork of https://github.com/xuranw/MuSiC. It contains the following modifications:

• Compatibility with sparse matrices using: dgCMatrix objects in R.

If you want to install the MuSiC library with these modifications you can use:

if("MuSiC" %in% rownames(installed.packages())){
  library(MuSiC)
}else{
  devtools::install_github( repo = "crhisto/MuSiC")
  library(MuSiC)
}

Also, you must use the following libraries with support of sparse matrix (dgCMatrix) for large scRNA-seq datasets:

• Biobase: https://github.com/crhisto/Biobase
• xbioc: https://github.com/crhisto/xbioc