muscat
This is the development version of muscat; for the stable release version, see muscat.
All Bioconductor versions of muscat
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10
Multi-sample multi-group scRNA-seq data analysis tools
Bioconductor version: 3.24 · Package version: 1.27.4
`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], Jeroen Gilis [aut], Davide Risso [aut], Lieven Clement [aut], Mark D. Robinson [aut, fnd]
Maintainer: Helena L. Crowell <helena at crowell.eu>
Citation
From within R, enter citation("muscat"):
Helena L. Crowell, Pierre-Luc Germain, Charlotte Soneson, Anthony Sonrel, Jeroen Gilis, Davide Risso, Lieven Clement, Mark D. Robinson. muscat: Multi-sample multi-group scRNA-seq data analysis tools. doi:10.18129/B9.bioc.muscat, R package version 1.27.4, https://bioconductor.org/packages/muscat.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("muscat")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.27.4 |
| License | GPL-3 |
| URL | https://github.com/HelenaLC/muscat |
| Bug Reports | https://github.com/HelenaLC/muscat/issues |
| Last updated | 2026-07-06 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 years) |
| Downloads rank | 245 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization |
| Package Short Url | https://bioconductor.org/packages/muscat/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("muscat")| Differential state analysis with muscat | HTML | R Script |
| Simulating complex design scRNA-seq data with muscat | HTML | R Script |
| Differential detection analysis | HTML | R Script |
| Increasing power with bulk-based hypothesis weighing (bbhw) | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | muscat_1.27.4.tar.gz |
| Windows binary (x86_64) | muscat_1.27.4.zip |
| macOS binary (arm64) | muscat_1.27.4.tgz |
| macOS binary (x86_64) | muscat_1.27.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/muscat |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/muscat |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5)
Imports: BiocParallel, blme, ComplexHeatmap, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, MatrixGenerics, matrixStats, methods, progress, rlang, S4Vectors, scales, scater, scuttle, scrapper, stats, SingleCellExperiment, SummarizedExperiment, variancePartition
Suggests: BiocStyle, countsimQC, DESeq2, AnnotationHub, ExperimentHub, iCOBRA, IHW, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, sctransform, statmod, stageR, testthat, tidyr, UpSetR
Reverse dependencies
Suggests Me (4): crumblr, DeeDeeExperiment, dreamlet, muscData