MAST
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MAST.
Model-based Analysis of Single Cell Transcriptomics
Bioconductor version: 3.9
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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, RNASeq, SingleCell, Software, Transcriptomics |
| Version | 1.10.0 |
| 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, blme, 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), 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, 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.
| Source Package | MAST_1.10.0.tar.gz |
| Windows Binary | MAST_1.10.0.zip |
| Mac OS X 10.11 (El Capitan) | MAST_1.10.0.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 3.9 | Source Archive |