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

DOI: 10.18129/B9.bioc.MAST

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>

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

Installation

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


if (!require("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")

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 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 1.8.2

In Bioconductor since BioC 3.4 (R-3.3) (7.5 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

System Requirements

URL https://github.com/RGLab/MAST/

Bug Reports https://github.com/RGLab/MAST/issues

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

Linking To

Enhances

Depends On Me

Imports Me celaref, singleCellTK

Suggests Me clusterExperiment

Links To Me

Build Report 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

Bioc Package Browser https://code.bioconductor.org/browse/MAST/

Package Short Url https://bioconductor.org/packages/MAST/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.8 Source Archive