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This is the development version of muscat; for the stable release version, see muscat.

Multi-sample multi-group scRNA-seq data analysis tools

Bioconductor version: Development (3.19)

`muscat` provides various methods and visualization tools for DS analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated “pseudobulk” data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.

Author: Helena L. Crowell [aut, cre] , Pierre-Luc Germain [aut], Charlotte Soneson [aut], Anthony Sonrel [aut], Mark D. Robinson [aut, fnd]

Maintainer: Helena L. Crowell <helena at crowell.eu>

Citation (from within R, enter citation("muscat")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1. DS analysis HTML R Script
2. Data simulation HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 4.3)
Imports BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis
System Requirements
URL https://github.com/HelenaLC/muscat
Bug Reports https://github.com/HelenaLC/muscat/issues
See More
Suggests BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, testthat, UpSetR
Linking To
Depends On Me
Imports Me
Suggests Me dreamlet, muscData
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package muscat_1.17.0.tar.gz
Windows Binary muscat_1.17.0.zip (64-bit only)
macOS Binary (x86_64) muscat_1.17.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/muscat
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/muscat
Bioc Package Browser https://code.bioconductor.org/browse/muscat/
Package Short Url https://bioconductor.org/packages/muscat/
Package Downloads Report Download Stats