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 (3.22)
`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")):
Installation
To install this package, start R (version "4.5") 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 |
| 3. Differential detection | HTML | R Script |
| 4. Increasing power with bulk-based hypothesis weighing | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization |
| Version | 1.23.2 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 years) |
| License | GPL-3 |
| Depends | R (>= 4.5) |
| Imports | BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, IHW, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, rlang, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition |
| System Requirements | |
| URL | https://github.com/HelenaLC/muscat |
| Bug Reports | https://github.com/HelenaLC/muscat/issues |
See More
| Suggests | BiocStyle, cowplot, countsimQC, AnnotationHub, ExperimentHub, iCOBRA, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, stageR, testthat, tidyr, UpSetR |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | crumblr, 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_1.23.2.tar.gz |
| Windows Binary (x86_64) | muscat_1.23.0.zip |
| macOS Binary (x86_64) | muscat_1.23.2.tgz |
| macOS Binary (arm64) | muscat_1.23.2.tgz |
| 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 |