Package: muscat
Title: Multi-sample multi-group scRNA-seq data analysis tools
Description: `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.
Type: Package
Version: 1.27.2
Depends: R (>= 4.5)
Authors@R: c(
	person("Helena L.", "Crowell", 
	    role=c("aut", "cre"),
	    email="helena@crowell.eu", 
	    comment=c(ORCID="0000-0002-4801-1767")), 
	person("Pierre-Luc", "Germain", role="aut"),
	person("Charlotte", "Soneson", role="aut"),
	person("Anthony", "Sonrel", role="aut"),
	person("Jeroen", "Gilis", role="aut"),
	person("Davide", "Risso", role="aut"),
	person("Lieven", "Clement", role="aut"),
	person("Mark D.", "Robinson", role=c("aut", "fnd"), 
	    email="mark.robinson@imls.uzh.ch"))
Imports: BiocParallel, blme, ComplexHeatmap, dplyr, edgeR, ggplot2,
        glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix,
        MatrixGenerics, matrixStats, methods, progress, rlang,
        S4Vectors, scales, scater, scuttle, stats,
        SingleCellExperiment, SummarizedExperiment, variancePartition
Suggests: BiocStyle, countsimQC, DESeq2, AnnotationHub, ExperimentHub,
        iCOBRA, IHW, knitr, patchwork, phylogram, RColorBrewer,
        reshape2, rmarkdown, sctransform, statmod, stageR, testthat,
        tidyr, UpSetR
biocViews: ImmunoOncology, DifferentialExpression, Sequencing,
        SingleCell, Software, StatisticalMethod, Visualization
License: GPL-3
VignetteBuilder: knitr
Encoding: UTF-8
URL: https://github.com/HelenaLC/muscat
BugReports: https://github.com/HelenaLC/muscat/issues
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake make libicu-dev libpng-dev perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-04 07:02:36 UTC
RemoteUrl: https://github.com/bioc/muscat
RemoteRef: HEAD
RemoteSha: 85db6262819eedd071811d23accad1383af36103
NeedsCompilation: no
Packaged: 2026-07-04 09:06:25 UTC; root
Author: Helena L. Crowell [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4801-1767>),
  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@crowell.eu>