MAST

DOI: 10.18129/B9.bioc.MAST    

Model-based Analysis of Single Cell Transcriptomics

Bioconductor version: Release (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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MAST", version = "3.8")

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 1.8.0
In Bioconductor since BioC 3.4 (R-3.3) (2 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_1.8.0.tar.gz
Windows Binary MAST_1.8.0.zip
Mac OS X 10.11 (El Capitan) MAST_1.8.0.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 http://bioconductor.org/packages/MAST/
Package Downloads Report Download Stats

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