muscat

This is the development version of muscat; for the stable release version, see muscat.

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


Bioconductor version: Development (3.20)

`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], Jeroen Gilis [aut], Davide Risso [aut], Lieven Clement [aut], Mark D. Robinson [aut, fnd]

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

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("muscat")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization
Version 1.19.1
In Bioconductor since BioC 3.10 (R-3.6) (5 years)
License GPL-3
Depends R (>= 4.4)
Imports BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, rlang, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis
System Requirements
URL https://github.com/HelenaLC/muscat
Bug Reports https://github.com/HelenaLC/muscat/issues
See More
Suggests BiocStyle, countsimQC, ExperimentHub, iCOBRA, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, stageR, testthat, UpSetR
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64) muscat_1.19.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/muscat
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/muscat
Bioc Package Browser https://code.bioconductor.org/browse/muscat/
Package Short Url https://bioconductor.org/packages/muscat/
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