[](https://travis-ci.org/RGLab/MAST) 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. Examples and vignettes ------------ 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')` or `vignette('MAST-intro')`. New Features and announcements ------------ - MAST has been ported to use `SingleCellExperiment` under the hood, and is in [Bioconductor](http://bioconductor.org/packages/release/bioc/html/MAST.html). - We now make an effort to track assay contents (counts vs log counts). This should facilitate interaction with Scater and SCRAN. The older version will remain accessible under branch *MASTClassic* Getting Help ---------------- For general questions, please submit a question to the [bioconductor support site](https://support.bioconductor.org/t/MAST/) so that others can benefit from the discussion. For bug reports (something seems broken): open a bug report [here](https://github.com/RGLab/MAST/issues). Citation ---------------- 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](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0844-5) G Finak, A McDavid, M Yajima, J Deng, V Gersuk, AK Shalek, CK Slichter et al Genome biology 16 (1), 278 Installation Instructions ------------ If you have previously installed the package `SingleCellAssay` you will want to remove it as `MAST` supercedes `SingleCellAssay`. (If both `MAST` and `SingleCellAssay` are attached, opaque S4 dispatch errors will result.) Remove it with: remove.packages('SingleCellAssay') Then you may install or update `MAST` with: install.packages("BiocManager") # Needed to install all Bioconductor packages BiocManager::install("MAST") Converting old MASTClassic SingleCellAssay objects -------- If you have data analyzed using MASTClassic, you can convert objects from MASTClassic format to the new format based on SingleCellExperiment using `convertMastClassicToSingleCellAssay()`.