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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
| 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 | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | GPL-3 |
| Depends | R (>= 4.6) |
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/muscat/ |
| Package Short Url | https://bioconductor.org/packages/muscat/ |
| Package Downloads Report | Download Stats |