Package: MAST 1.39.0

Andrew McDavid

MAST: Model-based Analysis of Single Cell Transcriptomics

Methods and models for handling zero-inflated single cell assay data.

Authors:Andrew McDavid [aut, cre], Greg Finak [aut], Masanao Yajima [aut]

MAST_1.39.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MAST/json (API)

# Install 'MAST' in R:
install.packages('MAST', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rglab/mast/issues

Datasets:

On BioConductor:MAST-1.39.0(bioc 3.24)MAST-1.38.0(bioc 3.23)

geneexpressiondifferentialexpressiongenesetenrichmentrnaseqtranscriptomicssinglecell

12.69 score 265 stars 6 packages 2.5k scripts 668 mentions 59 exports 47 dependencies

Last updated from:33e2f7332b. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING303
linux-devel-x86_64NOTE495
source / vignettesOK464
linux-release-x86_64NOTE481
macos-release-arm64NOTE244
macos-oldrel-arm64NOTE242
windows-develNOTE632
windows-releaseNOTE600
windows-oldrelNOTE659
wasm-releaseOK276

Exports:assay_idxbootVcov1burdenOfFilteringcalcZCoefficientHypothesiscolData<-collectResidualscombined_residuals_hookcomputeEtFromCtcondmeancondSdcontinuous_residuals_hookconvertMASTClassicToSingleCellAssaydefaultPriordeviance_residuals_hookdiscrete_residuals_hookexpavgfilterLowExpressedGenesfitted_phatfreqFromFlatDFFromMatrixgetConcordancegetLogFCgetrcgetssgetwellKeygetwssgsea_controlgseaAfterBoothushWarningHypothesisimputeinvlogitlogFClogLiklogmeanLRTlrTestmast_filtermelt.SingleCellAssaynumexppartialScorepbootVcov1plotSCAConcordanceprimerAverageread.fluidigmSceToSingleCellAssayse.coefshowsplitstat_ellsubsetsummarythresholdSCRNACountMatrixupdatevcovwaldTestzlm

Dependencies:abindBiobaseBiocGenericsclicpp11crayondata.tableDelayedArrayfarvergenericsGenomicRangesggplot2gluegtablehmsIRangesisobandlabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspkgconfigplyrprettyunitsprogressR6RColorBrewerRcppreshape2rlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraystringistringrSummarizedExperimentvctrsviridisLitewithrXVector

MAST Intro
Philosophy | Internals | Statistical Testing | Examples | Reading Data | Filtering | Significance testing under the Hurdle model | Two-sample Likelihood Ratio Test | Use with single cell RNA-sequencing data | A Comment on Implementation Details | References
Rendered fromMAST-Intro.Rmdusingknitr::rmarkdown

Last update: 2025-10-14
Started: 2017-08-23

Interoptability between MAST and SingleCellExperiment-derived packages.
Introduction | Log-transformation is expected in MAST | Examples | From MAST to Scater | From scater to MAST | Sparse matrix and HDF5 support | MAST and ZINB-wave | Using MAST to characterizing genes that drive the factors | References
Rendered fromMAST-interoperability.Rmdusingknitr::rmarkdown

Last update: 2023-04-20
Started: 2018-05-16

Using MAST with RNASeq: MAIT Analysis.
Overview | Loading and transforming data | Exploratory Data Analysis | Filtering | Recalculating the cellular detection rate (ngeneson) | PCA on filtered cells | Exercises on loading and transforming data | Adaptive thresholding | Exercises on thresholding | Differential Expression using a Hurdle model | Visualization of 50 most differentially expressed genes | Visualizing both components | Heatmap of MAITs based on most differentially expressed genes | Exercises on hurdle model differential expression | Residuals | Gene Set Enrichment Analysis
Rendered fromMAITAnalysis.Rmdusingknitr::rmarkdown

Last update: 2020-03-21
Started: 2016-10-12

Readme and manuals

Help Manual

Help pageTopics
MAST: Model-based Analysis of Single- cell TranscriptomicsMAST-package MAST
Apply a vectorized binary operation recycling over last dimensionapplyFlat
Wrapper for bayesian GLMBayesGLMlike-class
Get Z or T statistics and P values after running gseaAfterBootcalcZ
Replace 'colData'colData<-,SingleCellAssay,DataFrame-method
Residual hooks and collection methodscollectResiduals combined_residuals_hook continuous_residuals_hook deviance_residuals_hook discrete_residuals_hook fitted_phat partialScore
Compute the Et from the CtcomputeEtFromCt
Convert a MASTClassic SingleCellAssayconvertMASTClassicToSingleCellAssay
Extract the inter-gene covariance matrices for continuous and discrete components of a MAST model for a given coefficient from bootstrap replicatesCovFromBoots
Initialize a prior to be used a prior for BayeGLMlike/BayesGLMlike2defaultPrior
Degrees of freedom of Zero inflated modeldof dof,GLMlike-method dof,LMERlike-method
Drop specified dimension from an arrayDrop
Estimate hyperparameters for hierarchical variance model for continuous componentebayes
Exponential averageexpavg
Filter low-expressing genesfilterLowExpressedGenes
fit a zero-inflated regressionfit fit,BayesGLMlike,missing-method fit,GLMlike,missing-method fit,LMERlike,missing-method
Summary statistics for genes in an experimentcondmean condSd freq numexp
Construct a SingleCellAssay (or derived subclass) from a `flat` (melted) data.frame/data.tableFluidigmAssay FromFlatDF SingleCellAssay
Construct a SingleCellAssay from a matrix or array of expressionFromMatrix
Get the concordance between two experimentsgetConcordance getrc getss getwss
Accessor for wellKeygetwellKey getwellKey,SingleCellAssay-method
Wrapper for regular glm/lmGLMlike-class vcov,GLMlike-method
Gene set analysis for hurdle modelgseaAfterBoot gsea_control
An S4 class for Gene Set Enrichment outputGSEATests-class
Selectively muffle warnings based on outputhushWarning
Describe a linear model hypothesis to be testedCoefficientHypothesis Hypothesis
impute missing continuous expression for plottingimpute
Influence bayesglm objectinfluence.bayesglm
Inverse of logistic transformationinvlogit
Wrapper for lmer/glmercoef,LMERlike-method LMERlike-class logLik,LMERlike-method update,LMERlike-method vcov,LMERlike-method
Linear Model-like ClassLMlike-class logLik,GLMlike-method lrTest,LMlike,character-method lrTest,LMlike,CoefficientHypothesis-method lrTest,LMlike,Hypothesis-method lrTest,LMlike,matrix-method summary,LMlike-method update,LMlike-method waldTest,LMlike,CoefficientHypothesis-method waldTest,LMlike,matrix-method
Calculate log-fold changes from hurdle model componentsgetLogFC logFC
Log meanlogmean
Likelihood Ratio Tests for SingleCellAssaysLRT LRT,SingleCellAssay,character-method
Run a likelihood-ratio testlrTest
Likelihood ratio testlrTest,ZlmFit,character-method
Default 'assay' returnedassay,SingleCellAssay,missing-method assay_idx defaultAssay magic_assay_names
MAITs data set, RNASeqmaits
Filter a SingleCellAssayburdenOfFiltering mast_filter
Defunct functions in package `MAST`cData exprs fData filter MAST-defunct
Combine lists, preferentially taking elements from x if there are duplicate namesmeld_list_left
"Melt" a 'SingleCellAssay' matrixmelt.SingleCellAssay
Model matrix accessormodel.matrix model.matrix,LMlike-method
Replace model matrixmodel.matrix<-
Makes a nice BiPlotmyBiplot
Instantiate a class, but warn rather than error for badly named slotsnew_with_repaired_slots
Bootstrap a zlmfitbootVcov1 pbootVcov1
Plot cutpoints and densities for thresholdingplot.thresholdSCRNACountMatrix
Plot a likelihood ratio test objectplotlrt
Concordance plots of filtered single vs n-cell assaysplotSCAConcordance
Return predictions from a ZlmFit object.predict.ZlmFit
Predicted signaturespredicted_sig
Average expression values for duplicated/redundant genesprimerAverage
Print summary of a ZlmFitprint.summaryZlmFit
Reads a Fluidigm Biomark (c. 2011) raw data file (or set of files)read.fluidigm
Remove the left hand side (response) from a formularemoveResponse
rstandard for bayesglm objects.rstandard.bayesglm
Coerce a SingleCellExperiment to some class defined in MASTSceToSingleCellAssay
Return coefficient standard errorsse.coef
showshow,LMlike-method show,ZlmFit-method
Split into 'list'split,SingleCellAssay,character-method split,SingleCellAssay,factor-method split,SingleCellAssay,list-method
Plot confidence ellipse in 2Dstat_ell
Subset a 'SingleCellAssay' by cells (columns)subset,SingleCellAssay-method
Return programmatically useful summary of a fitsummarize
Summarize gene set enrichment testssummary,GSEATests-method
Summarize model features from a 'ZlmFit' object"summary-ZlmFit", "summary.ZlmFit" "ZlmFit-summary", summary,ZlmFit-method
Summarize the effect of thresholdingprint.summaryThresholdSCRNA summary.thresholdSCRNACountMatrix
Threshold a count matrix using an adaptive threshold.thresholdSCRNACountMatrix
Vbeta Data Setvbeta
Vbeta Data Set, FluidigmAssayvbetaFA
Run a Wald testwaldTest
Wald testwaldTest,ZlmFit,matrix-method
Make matrix of continuous expression values, orthogonal to discretexform
Zero-inflated regression for SingleCellAssayzlm zlm.SingleCellAssay
An S4 class to hold the output of a call to zlmcoef,ZlmFit-method lrTest,ZlmFit,CoefficientHypothesis-method lrTest,ZlmFit,Hypothesis-method lrTest,ZlmFit,matrix-method se.coef,ZlmFit-method vcov,ZlmFit-method waldTest,ZlmFit,CoefficientHypothesis-method waldTest,ZlmFit,Hypothesis-method ZlmFit ZlmFit-class