muscat

DOI: 10.18129/B9.bioc.muscat    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see muscat.

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

Bioconductor version: 3.12

`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], Mark D. Robinson [aut, fnd]

Maintainer: Helena L. Crowell <helena.crowell at uzh.ch>

Installation

To install this package, start R (version "4.0") and enter:

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

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")

 

HTML	R Script	1. DS analysis
HTML	R Script	2. Data simulation
PDF		Reference Manual

Details

biocViews	DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.10 (R-3.6) (1.5 years)
License	GPL (>= 2)
Depends	R (>= 4.0)
Imports	BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, S4Vectors, scales, scater, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis
LinkingTo
Suggests	BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, testthat, UpSetR
SystemRequirements
Enhances
URL	https://github.com/HelenaLC/muscat
BugReports	https://github.com/HelenaLC/muscat/issues
Depends On Me
Imports Me
Suggests Me	muscData
Links To Me
Build Report

Package Archives

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

Source Package	muscat_1.4.0.tar.gz
Windows Binary	muscat_1.4.0.zip
macOS 10.13 (High Sierra)	muscat_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/muscat
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/muscat
Package Short Url	https://bioconductor.org/packages/muscat/
Package Downloads Report	Download Stats