DOI: 10.18129/B9.bioc.muscat  

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 (3.18)

`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")):


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biocViews DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization
Version 1.15.0
In Bioconductor since BioC 3.10 (R-3.6) (3.5 years)
License GPL-3
Depends R (>= 4.2)
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
Suggests BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, testthat, UpSetR
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