DOI: 10.18129/B9.bioc.muscat    

This is the development version of muscat; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.10)

`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], Charlotte Soneson [aut], Pierre-Luc Germain [aut], Mark D. Robinson [aut, fnd]

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

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


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biocViews DifferentialExpression, Sequencing, SingleCell, Software, StatisticalMethod, Visualization
Version 0.99.9
In Bioconductor since BioC 3.10 (R-3.6)
License GPL (>= 2)
Depends R (>= 3.6), scater(>= 1.13)
Imports BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, doParallel, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, magrittr, Matrix, matrixStats, methods, parallel, progress, purrr, reshape2, scales, sctransform, stats, SingleCellExperiment, SummarizedExperiment, S4Vectors, tibble, variancePartition, viridis
Suggests BiocStyle, cowplot, ExperimentHub, knitr, RColorBrewer, rmarkdown, testthat, UpSetR
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