muscat

DOI: 10.18129/B9.bioc.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 (3.18)

`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 at crowell.eu>

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

Installation

To install this package, start R (version "4.3") 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

PDF   Reference Manual

Details

biocViews DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization
Version 1.15.0
In Bioconductor since BioC 3.10 (R-3.6) (3.5 years)
License GPL-3
Depends R (>= 4.2)
Imports BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis
LinkingTo
Suggests BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, 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
Windows Binary
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
Package Short Url https://bioconductor.org/packages/muscat/
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