README.md
In MAST: Model-based Analysis of Single Cell Transcriptomics

MAST: Model-based Analysis of Single-cell Transcriptomics

MAST fits two-part, generalized linear models that are specially adapted for bimodal and/or zero-inflated single cell gene expression data.

MAST supports:

Easy importing, subsetting and manipulation of expression matrices
Filtering of low-quality cells
Adaptive thresholding of background noise
Tests for univariate differential expression, with adjustment for covariates
Gene set enrichment analysis, corrected for covariates and gene-gene correlations
Exploration of gene-gene correlations and co-expression

Vignettes are available in the package via vignette('MAITAnalysis'), vignette('MAST-intro') or vignette('MAST-interoperability').

MAST has been ported to use SingleCellExperiment under the hood, and is in Bioconductor.
We now make an effort to track assay contents (counts vs log counts). This should facilitate interaction with Scater and SCRAN.

For general questions, please submit a question to the bioconductor support site so that others can benefit from the discussion.

For bug reports (something seems broken): open a bug report here.

This version available here on github may only properly function if you are running Bioconductor Devel, which is not something you will want to run for existing analyses! Instead follow instructions below.

You may install or update MAST with:

install.packages("BiocManager") # Needed to install all Bioconductor packages
BiocManager::install("MAST")

If you find MAST useful in your work, please consider citing the paper: MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data G Finak, A McDavid, M Yajima, J Deng, V Gersuk, AK Shalek, CK Slichter et al Genome biology 16 (1), 278

The version that was used in the Genome Biology paper is accesible under the branch MASTClassic.

If you have data analyzed using MASTClassic, you can convert objects from MASTClassic format to the new format based on SingleCellExperiment using convertMastClassicToSingleCellAssay().