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: 1.25.0
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, 
	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
git_url: https://git.bioconductor.org/packages/muscat
git_branch: devel
git_last_commit: 7a0ebff
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
