Registration Open for Bioc2024 July 24-26


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

Bioconductor version: Release (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>

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


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

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


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 1.18.0
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
Bug Reports
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
Build Report Build Report

Package Archives

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

Source Package muscat_1.18.0.tar.gz
Windows Binary
macOS Binary (x86_64) muscat_1.18.0.tgz
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats