MAST

This is the development version of MAST; for the stable release version, see MAST.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

Model-based Analysis of Single Cell Transcriptomics

Bioconductor version: Development (3.24)

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.n.mcdavid at gmail.com>

Citation (from within R, enter citation("MAST")):

Andrew McDavid, Greg Finak, Masanao Yajima. MAST: Model-based Analysis of Single Cell Transcriptomics. doi:10.18129/B9.bioc.MAST, R package version 1.39.0, https://bioconductor.org/packages/MAST.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, RNASeq, SingleCell, Software, Transcriptomics
Version	1.39.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 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, Matrix
System Requirements
URL	https://github.com/RGLab/MAST/
Bug Reports	https://github.com/RGLab/MAST/issues

Suggests	knitr, rmarkdown, testthat, lme4 (>= 1.0), blme, roxygen2 (> 6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater, DelayedArray, HDF5Array, zinbwave, dplyr
Linking To
Enhances
Depends On Me	POWSC
Imports Me	benchdamic, celaref, DWLS, singleCellTK
Suggests Me	clusterExperiment, DAssemble, EWCE, Seurat, SeuratExplorer, XYomics
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	MAST_1.39.0.tar.gz
Windows Binary (x86_64)	MAST_1.39.0.zip
macOS Binary (big-sur-x86_64)	MAST_1.39.0.tgz
macOS Binary (sonoma-arm64)	MAST_1.39.0.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	https://bioconductor.org/packages/MAST/
Package Downloads Report	Download Stats