MAST

DOI: 10.18129/B9.bioc.MAST    

Model-based Analysis of Single Cell Transcriptomics

Bioconductor version: Release (3.7)

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 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")

 

HTML R Script An Introduction to MAST
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 1.6.1
In Bioconductor since BioC 3.4 (R-3.3) (1.5 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)
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
SystemRequirements
Enhances
URL https://github.com/RGLab/MAST/
BugReports https://github.com/RGLab/MAST/issues
Depends On Me
Imports Me singleCellTK
Suggests Me clusterExperiment
Build Report  

Package Archives

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

Source Package MAST_1.6.1.tar.gz
Windows Binary MAST_1.6.1.zip
Mac OS X 10.11 (El Capitan) MAST_1.6.1.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
Old Source Packages for BioC 3.7 Source Archive

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