MuSiC

MuSiC is an analysis toolkit for single-cell RNA-Seq experiments. To use this package, you will need the R statistical computing environment (version 3.0 or later) and several packages available through Bioconductor and CRAN.

Update (09/26/2022)

MuSiC (v1.0.0) now support SingleCellExperiment class as single cell reference!
Please See updated Tutorial for guidance!

Update (09/26/2022)

MuSiC2 is available! You can use MuSiC2 for cell type deconvolution for multi-condition bulk RNA-seq data.
MuSiC2 functions can be accessed with either latest version of MuSiC(v1.0.0) or installed from this github repo of Dr. Jiaxin Fan.

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

MuSiC2 is an iterative algorithm aiming to improve cell type deconvolution for bulk RNA-seq data using scRNA-seq data as reference when the bulk data are generated from samples with multiple clinical conditions where at least one condition is different from the scRNA-seq reference.

How to cite MuSiC

Please cite the following publications:

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

MuSiC2: cell type deconvolution for multi-condition bulk RNA-seq data
J. Fan, Y. Lyu, Q. Zhang, X. Wang, R. Xiao, M. Li
Briefings in Bioinformatics. 2022 https://doi.org/10.1093/bib/bbac430

Installation

Both MuSiC and MuSiC2 functions are available in one package.

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

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

# load
library(MuSiC)

More Information

Please see Tutorials for MuSiC and MuSiC2.