muscat
This is the released version of muscat; for the devel version, see muscat.
Multi-sample multi-group scRNA-seq data analysis tools
Bioconductor version: Release (3.23)
`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], Jeroen Gilis [aut], Davide Risso [aut], Lieven Clement [aut], Mark D. Robinson [aut, fnd]
Maintainer: Helena L. Crowell <helena at crowell.eu>
citation("muscat")):Helena L. Crowell, Pierre-Luc Germain, Charlotte Soneson, Anthony Sonrel, Jeroen Gilis, Davide Risso, Lieven Clement, Mark D. Robinson. muscat: Multi-sample multi-group scRNA-seq data analysis tools. doi:10.18129/B9.bioc.muscat, R package version 1.26.0, https://bioconductor.org/packages/muscat.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("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")| "1. DS analysis" | HTML | R Script |
| "4. Increasing power with bulk-based hypothesis weighing" | HTML | R Script |
| "3. Differential detection" | HTML | R Script |
| "2. Data simulation" | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | GPL-3 |
| Depends | R (>= 4.5) |
| Imports | BiocParallel, blme, ComplexHeatmap, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, MatrixGenerics, matrixStats, methods, progress, rlang, S4Vectors, scales, scater, scuttle, stats, SingleCellExperiment, SummarizedExperiment, variancePartition |
| System Requirements | |
| URL | https://github.com/HelenaLC/muscat |
| Bug Reports | https://github.com/HelenaLC/muscat/issues |
See More
| Suggests | BiocStyle, countsimQC, DESeq2, AnnotationHub, ExperimentHub, iCOBRA, IHW, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, sctransform, statmod, stageR, testthat, tidyr, UpSetR |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | crumblr, DeeDeeExperiment, dreamlet, muscData |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | muscat_1.26.0.tar.gz |
| Windows Binary (x86_64) | muscat_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | muscat_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | muscat_1.26.0.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 |