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MAST

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MAST.

Model-based Analysis of Single Cell Transcriptomics

Bioconductor version: 3.10

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 "3.6") 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 Details biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, RNASeq, SingleCell, Software, Transcriptomics Version 1.12.0 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 See More 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, Matrix, HDF5Array Linking To Enhances Depends On Me Imports Me celaref, celda, singleCellTK Suggests Me clusterExperiment Links To Me Build Report Build Report Package Archives

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

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