muscat

DOI:10.18129/B9.bioc.muscat

Multi-sample multi-group scRNA-seq data analysis tools

Bioconductor版本:版本(3.15)

`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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("muscat")

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

查看documentation for the version of this package installed in your system, start R and enter:

browseVignettes("muscat")

HTML	R Script	1. DS analysis
HTML	R Script	2. Data simulation
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression,ImmunoOncology,Sequencing,SingleCell,Software,StatisticalMethod,Visualization
Version	1.10.1
In Bioconductor since	BioC 3.10 (R-3.6) (3 years)
License	GPL-3
Depends	R (>= 4.2)
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
LinkingTo
Suggests	BiocStyle,countsimQC,cowplot,ExperimentHub,iCOBRA,knitr,phylogram,RColorBrewer,reshape2,rmarkdown,statmod,testthat,UpSetR
SystemRequirements
Enhances
URL	https://github.com/HelenaLC/muscat
BugReports	https://github.com/HelenaLC/muscat/issues
Depends On Me
Imports Me
Suggests Me	muscData
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	muscat_1.10.1.tar.gz
Windows Binary	muscat_1.10.1.zip
macOS Binary (x86_64)	muscat_1.10.1.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	//www.andersvercelli.com/packages/muscat/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive