muscat

DOI: 10.18129/B9.bioc.muscat    

This is the development version of muscat; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.10)

`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], Charlotte Soneson [aut], Pierre-Luc Germain [aut], Mark D. Robinson [aut, fnd]

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

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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Details

biocViews DifferentialExpression, Sequencing, SingleCell, Software, StatisticalMethod, Visualization
Version 0.99.9
In Bioconductor since BioC 3.10 (R-3.6)
License GPL (>= 2)
Depends R (>= 3.6), scater(>= 1.13)
Imports BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, doParallel, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, magrittr, Matrix, matrixStats, methods, parallel, progress, purrr, reshape2, scales, sctransform, stats, SingleCellExperiment, SummarizedExperiment, S4Vectors, tibble, variancePartition, viridis
LinkingTo
Suggests BiocStyle, cowplot, ExperimentHub, knitr, RColorBrewer, rmarkdown, testthat, UpSetR
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package muscat_0.99.9.tar.gz
Windows Binary muscat_0.99.9.zip
Mac OS X 10.11 (El Capitan) muscat_0.99.9.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

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