MAST
Model-based Analysis of Single Cell Transcriptomics
Bioconductor version: 3.24 · Package version: 1.39.0
Methods and models for handling zero-inflated single cell assay data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MAST")Details
| Maintainer | Andrew McDavid <andrew.n.mcdavid@gmail.com> |
| Author | Andrew McDavid [aut, cre], Greg Finak [aut], Masanao Yajima [aut] |
| License | GPL(>= 2) |
| URL | https://github.com/RGLab/MAST/ |
| Bug Reports | https://github.com/RGLab/MAST/issues |
| Downloads rank | 3227 |
| Source branch | devel |
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, RNASeq, SingleCell, Software, Transcriptomics |
Documentation
- MAST Intro
- Interoptability between MAST and SingleCellExperiment-derived packages.
- Using MAST with RNASeq: MAIT Analysis.
Download
Follow the installation instructions to use this package in your R session.
| Source package | MAST_1.39.0.tar.gz |
| Windows binary (x86_64) | MAST_1.39.0.zip |
| macOS binary (arm64) | MAST_1.39.0.tgz |
| macOS binary (x86_64) | MAST_1.39.0.tgz |
Dependencies
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, Matrix
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, HDF5Array, zinbwave, dplyr
Reverse dependencies
Depends On Me (1): POWSC
Imports Me (4): benchdamic, celaref, DWLS, singleCellTK
Suggests Me (6): clusterExperiment, DAssemble, EWCE, Seurat, SeuratExplorer, XYomics