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