To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MAST")

In most cases, you don't need to download the package archive at all.

MAST

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MAST.

Model-based Analysis of Single Cell Transcriptomics

Bioconductor version: 3.4

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

Author: Andrew McDavid <Andrew_McDavid at urmc.rochester.edu>, Greg Finak <gfinak at fredhutch.org>, Masanao Yajima <myajima at fredhutch.org>

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MAST")

Documentation

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

browseVignettes("MAST")
PDF R Script MAST-intro
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 1.0.5
In Bioconductor since BioC 3.4 (R-3.3) (0.5 years)
License GPL(>= 2)
Depends SummarizedExperiment, R (>= 3.3)
Imports Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr, stringr, abind, methods, parallel, reshape2, stats, stats4, graphics, utils
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
SystemRequirements
Enhances
URL https://github.com/RGLab/MAST/
BugReports https://github.com/RGLab/MAST/issues
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source MAST_1.0.5.tar.gz
Windows Binary MAST_1.0.5.zip
Mac OS X 10.9 (Mavericks) MAST_1.0.5.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/MAST/tree/release-3.4
Package Short Url http://bioconductor.org/packages/MAST/
Package Downloads Report Download Stats

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