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 (3.21)

`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] (ORCID: ), 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 "4.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("muscat")

1. DS analysis	HTML	R Script
2. Data simulation	HTML	R Script
3. Differential detection	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization
Version	1.21.0
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

Suggests	BiocStyle, countsimQC, ExperimentHub, iCOBRA, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, stageR, testthat, UpSetR
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	dreamlet, muscData
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	muscat_1.21.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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/
Package Downloads Report	Download Stats