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: 1.24.0
Depends: R (>= 4.4)
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, data.table, DESeq2, dplyr,
        edgeR, ggplot2, glmmTMB, grDevices, grid, IHW, limma, lmerTest,
        lme4, Matrix, matrixStats, methods, progress, purrr, rlang,
        S4Vectors, scales, scater, scuttle, sctransform, stats,
        SingleCellExperiment, SummarizedExperiment, variancePartition
Suggests: BiocStyle, cowplot, countsimQC, AnnotationHub, ExperimentHub,
        iCOBRA, knitr, patchwork, phylogram, RColorBrewer, reshape2,
        rmarkdown, statmod, stageR, testthat, tidyr, UpSetR
biocViews: ImmunoOncology, DifferentialExpression, Sequencing,
        SingleCell, Software, StatisticalMethod, Visualization
License: GPL-3
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Encoding: UTF-8
URL: https://github.com/HelenaLC/muscat
BugReports: https://github.com/HelenaLC/muscat/issues
Config/pak/sysreqs: libcairo2-dev cmake coinor-symphony
        coinor-libsymphony-dev libfontconfig1-dev libfreetype6-dev
        libfribidi-dev make libharfbuzz-dev libicu-dev libjpeg-dev
        libpng-dev libtiff-dev libwebp-dev perl zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:53:55 UTC
RemoteUrl: https://github.com/bioc/muscat
RemoteRef: RELEASE_3_22
RemoteSha: a6749ec3d8cfe61b23b93c6ac53bae3b74b748f7
NeedsCompilation: no
Packaged: 2026-02-23 09:11:45 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>
Built: R 4.5.2; ; 2026-02-23 09:14:18 UTC; windows
