DOI: 10.18129/B9.bioc.muscat  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see muscat.

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

Bioconductor version: 3.17

`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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HTML R Script 1. DS analysis
HTML R Script 2. Data simulation
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biocViews DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization
Version 1.14.0
In Bioconductor since BioC 3.10 (R-3.6) (4 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
Depends On Me
Imports Me
Suggests Me muscData
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