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], Mark D. Robinson [aut, fnd]
Maintainer: Helena L. Crowell <helena at crowell.eu>
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
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 |
Reference Manual | ||
NEWS | Text |
Details
biocViews | DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization |
Version | 1.19.0 |
In Bioconductor since | BioC 3.10 (R-3.6) (5 years) |
License | GPL-3 |
Depends | R (>= 4.3) |
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 |
System Requirements | |
URL | https://github.com/HelenaLC/muscat |
Bug Reports | https://github.com/HelenaLC/muscat/issues |
See More
Suggests | BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, 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_1.19.0.tar.gz |
Windows Binary | muscat_1.19.0.zip (64-bit only) |
macOS Binary (x86_64) | muscat_1.19.0.tgz |
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 |