MAST

DOI: 10.18129/B9.bioc.MAST    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see MAST.

Model-based Analysis of Single Cell Transcriptomics

Bioconductor version: 3.8

Methods and models for handling zero-inflated single cell assay data.

Author: Andrew McDavid [aut, cre], Greg Finak [aut], Masanao Yajima [aut]

Maintainer: Andrew McDavid <Andrew_McDavid at urmc.rochester.edu>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MAST")

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("MAST")

 

HTML	R Script	An Introduction to MAST
HTML	R Script	Interoptability between MAST and SingleCellExperiment-derived packages
HTML	R Script	Using MAST for filtering, differential expression and gene set enrichment in MAIT cells
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, RNASeq, SingleCell, Software, Transcriptomics
Version	1.8.2
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 years)
License	GPL(>= 2)
Depends	SingleCellExperiment(>= 1.2.0), R (>= 3.5)
Imports	Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr, stringr, abind, methods, parallel, reshape2, stats, stats4, graphics, utils, SummarizedExperiment(>= 1.5.3), progress
LinkingTo
Suggests	knitr, rmarkdown, testthat, lme4 (>= 1.0), roxygen2 (> 4.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater
SystemRequirements
Enhances
URL	https://github.com/RGLab/MAST/
BugReports	https://github.com/RGLab/MAST/issues
Depends On Me
Imports Me	celaref, singleCellTK
Suggests Me	clusterExperiment
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MAST_1.8.2.tar.gz
Windows Binary	MAST_1.8.2.zip
Mac OS X 10.11 (El Capitan)	MAST_1.8.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MAST
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MAST
Package Short Url	http://bioconductor.org/packages/MAST/
Package Downloads Report	Download Stats