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muscat
This is thedevelopment version of muscat; for the stable release version, seemuscat.
Multi-sample multi-group scRNA-seq data analysis tools
Bioconductor version: Development (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]
ORCID: 0000-0002-4801-1767, 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 "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("muscat")For older versions of R, please refer to the appropriateBioconductor 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 | 1.25.0 |
| 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,DeeDeeExperiment,dreamlet,muscData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | muscat_1.25.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | muscat_1.25.0.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 |