MAST: Model-based Analysis of Single Cell Transcriptomics

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

AuthorAndrew McDavid <Andrew_McDavid@urmc.rochester.edu>, Greg Finak <gfinak@fredhutch.org>, Masanao Yajima <myajima@fredhutch.org>
Date of publicationNone
MaintainerAndrew McDavid <Andrew_McDavid@urmc.rochester.edu>
LicenseGPL(>= 2)
Version1.0.5
https://github.com/RGLab/MAST/

View on Bioconductor

Man pages

applyFlat: Apply a vectorized binary operation recycling over last...

BayesGLMlike-class: Wrapper for bayesian GLM

bootVcov1: Bootstrap a zlmfit

calcZ: Get Z or T statistics and P values after running...

cData: Deprecated cell/feature data accessors/mutators

colData-set-SingleCellAssay-DataFrame-method: Replace 'colData'

collectResiduals: Residual hooks and collection methods

computeEtFromCt: Compute the Et from the Ct

condmean: Report the mean et value for each gene

condSd: Report standard deviation of et, for positive et for each...

convertMASTClassicToSingleCellAssay: Convert a MASTClassic SingleCellAssay

defaultPrior: Initialize a prior to be used a prior for...

dof: Degrees of freedom of Zero inflated model

Drop: Drop specified dimension from an array

ebayes: Estimate hyperparameters for hierarchical variance model for...

expavg: Exponential average

fData-methods: fData

featureData-methods: Accessor for featureData 'AnnotatedDataFrame'

filter: Filter a SingleCellAssay

filterLowExpressedGenes: Filter low-expressing genes

fit: fit a zero-inflated regression

freq: Report the proportion of expression for each gene

FromFlatDF: Construct a SingleCellAssay (or derived subclass) from a...

FromMatrix: Construct a SingleCellAssay from a matrix or array of...

getConcordance: getConcordance

getwellKey: Accessor for wellKey

GLMlike-class: Wrapper for regular glm/lm

gseaAfterBoot: Gene set analysis for hurdle model

GSEATests-class: An S4 class for Gene Set Enrichment output

hushWarning: Selectively muffle warnings based on output

Hypothesis: Describe a linear model hypothesis to be tested

impute: impute missing continuous expression for plotting

influence.bayesglm: Influence bayesglm object

invlogit: Inverse of logistic transformation

LMERlike-class: Wrapper for lmer/glmer

LMlike-class: Linear Model-like Class

logFC: Calculate log-fold changes from hurdle model components

logmean: Log mean

LRT: Likelihood Ratio Tests for SingleCellAssays

lrTest: Run a likelihood-ratio test

lrTest-ZlmFit-character-method: Likelihood ratio test

maits-dataset: MAITs data set, RNASeq

MAST-package: MAST: Model-based Analysis of Single- cell Transcriptomics

melt.SingleCellAssay: Melt a rectangular array

model.matrix: Model matrix accessor

model.matrix-set: Replace model matrix

myBiplot: Makes a nice BiPlot

numexp: Report number of expressing cells per gene

pbootVcov1: Bootstrap a zlmfit

plotlrt: Plot a likelihood ratio test object

plotSCAConcordance: Concordance plots of filtered single vs n-cell assays

plot.thresholdSCRNACountMatrix: Plot cutpoints and densities for thresholding

predict.ZlmFit: Return predictions from a ZlmFit object.

primerAverage: Average within duplicated genes/primers

print.summaryZlmFit: Print summary of a ZlmFit

read.fluidigm: read.fluidigm

removeResponse: Remove the left hand side (response) from a formula

rstandard.bayesglm: rstandard for bayesglm objects.

se.coef: Return coefficient standard errors

show: show

split-SingleCellAssay-character-method: Split into 'list'

stat_ell: Plot confidence ellipse in 2D

subset-SingleCellAssay-method: Subset a 'SingleCellAssay' by cells (columns)

summarize: Return programmatically useful summary of a fit

summary-GSEATests-method: Summarize gene set enrichment tests

summary.thresholdSCRNACountMatrix: Summarize the effect of thresholding

summary-ZlmFit-method: Summarize model features from a 'ZlmFit' object

thresholdSCRNACountMatrix: Threshold a count matrix using an adaptive threshold.

vbeta-dataset: Vbeta Data Set

vbetaFA-dataset: Vbeta Data Set, FluidigmAssay

waldTest: Run a Wald test

waldTest-ZlmFit-matrix-method: Wald test

xform: Make matrix of continuous expression values, orthogonal to...

zlm: Convenience function for running a zero-inflated regression

ZlmFit-class: An S4 class to hold the output of a call to zlm

zlm.SingleCellAssay: Zero-inflated regression for SingleCellAssay

Files in this package

MAST/DESCRIPTION
MAST/NAMESPACE
MAST/R
MAST/R/AllClasses.R MAST/R/AllGenerics.R MAST/R/Fluidigm-methods.R MAST/R/GSEA-by-boot.R MAST/R/Hypothesis.R MAST/R/LmWrapper.R MAST/R/MultidimensionalScaling.R MAST/R/RNASeqAssay-methods.R MAST/R/Readers.R MAST/R/SingleCellAssay-methods.R MAST/R/UtilityFunctions.R MAST/R/ZlmFit-bootstrap.R MAST/R/ZlmFit-logFC.R MAST/R/ZlmFit.R MAST/R/bayesglm.R MAST/R/convertMASTClassic.R MAST/R/ebayes-helpers.R MAST/R/filterEval.R MAST/R/helper-methods.R MAST/R/lmWrapper-bayesglm.R MAST/R/lmWrapper-glm.R MAST/R/lmWrapper-glmer.R MAST/R/lmWrapper-ridge.R MAST/R/lrtest.R MAST/R/predict.R MAST/R/stat_ell.R MAST/R/thresholdSCRNA.R MAST/R/zeroinf.R MAST/R/zlmHooks.R
MAST/README.md
MAST/build
MAST/build/vignette.rds
MAST/data
MAST/data/datalist
MAST/data/maits.RData
MAST/data/vbeta.RData
MAST/data/vbetaFA.RData
MAST/inst
MAST/inst/NEWS
MAST/inst/doc
MAST/inst/doc/MAITAnalysis.R
MAST/inst/doc/MAITAnalysis.Rmd
MAST/inst/doc/MAITAnalysis.html
MAST/inst/doc/MAST-intro.R
MAST/inst/doc/MAST-intro.Rnw
MAST/inst/doc/MAST-intro.pdf
MAST/inst/extdata
MAST/inst/extdata/BTM_for_GSEA_20131008.gmt
MAST/man
MAST/man/BayesGLMlike-class.Rd MAST/man/Drop.Rd MAST/man/FromFlatDF.Rd MAST/man/FromMatrix.Rd MAST/man/GLMlike-class.Rd MAST/man/GSEATests-class.Rd MAST/man/Hypothesis.Rd MAST/man/LMERlike-class.Rd MAST/man/LMlike-class.Rd MAST/man/LRT.Rd MAST/man/MAST-package.Rd MAST/man/ZlmFit-class.Rd MAST/man/applyFlat.Rd MAST/man/bootVcov1.Rd MAST/man/cData.Rd MAST/man/calcZ.Rd MAST/man/colData-set-SingleCellAssay-DataFrame-method.Rd MAST/man/collectResiduals.Rd MAST/man/computeEtFromCt.Rd MAST/man/condSd.Rd MAST/man/condmean.Rd MAST/man/convertMASTClassicToSingleCellAssay.Rd MAST/man/defaultPrior.Rd MAST/man/dof.Rd MAST/man/ebayes.Rd MAST/man/expavg.Rd MAST/man/fData-methods.Rd MAST/man/featureData-methods.Rd MAST/man/filter.Rd MAST/man/filterLowExpressedGenes.Rd MAST/man/fit.Rd MAST/man/freq.Rd MAST/man/getConcordance.Rd MAST/man/getwellKey.Rd MAST/man/gseaAfterBoot.Rd MAST/man/hushWarning.Rd MAST/man/impute.Rd MAST/man/influence.bayesglm.Rd MAST/man/invlogit.Rd MAST/man/logFC.Rd MAST/man/logmean.Rd MAST/man/lrTest-ZlmFit-character-method.Rd MAST/man/lrTest.Rd MAST/man/maits-dataset.Rd MAST/man/melt.SingleCellAssay.Rd MAST/man/model.matrix-set.Rd MAST/man/model.matrix.Rd MAST/man/myBiplot.Rd MAST/man/numexp.Rd MAST/man/pbootVcov1.Rd MAST/man/plot.thresholdSCRNACountMatrix.Rd MAST/man/plotSCAConcordance.Rd MAST/man/plotlrt.Rd MAST/man/predict.ZlmFit.Rd MAST/man/primerAverage.Rd MAST/man/print.summaryZlmFit.Rd MAST/man/read.fluidigm.Rd MAST/man/removeResponse.Rd MAST/man/rstandard.bayesglm.Rd MAST/man/se.coef.Rd MAST/man/show.Rd MAST/man/split-SingleCellAssay-character-method.Rd MAST/man/stat_ell.Rd MAST/man/subset-SingleCellAssay-method.Rd MAST/man/summarize.Rd MAST/man/summary-GSEATests-method.Rd MAST/man/summary-ZlmFit-method.Rd MAST/man/summary.thresholdSCRNACountMatrix.Rd MAST/man/thresholdSCRNACountMatrix.Rd MAST/man/vbeta-dataset.Rd MAST/man/vbetaFA-dataset.Rd MAST/man/waldTest-ZlmFit-matrix-method.Rd MAST/man/waldTest.Rd MAST/man/xform.Rd MAST/man/zlm.Rd MAST/man/zlm.SingleCellAssay.Rd
MAST/tests
MAST/tests/testthat
MAST/tests/testthat.R
MAST/tests/testthat/SingleCellAssay-Object-MASTClassic.RData
MAST/tests/testthat/common-lmWrapper-glm-tests.R
MAST/tests/testthat/common-lmWrapper-tests.R
MAST/tests/testthat/helper-vbeta-init.R
MAST/tests/testthat/test-AllClasses.R
MAST/tests/testthat/test-FluidigmAssay.R
MAST/tests/testthat/test-GSEA-by-boot.R
MAST/tests/testthat/test-Hypothesis.R
MAST/tests/testthat/test-SingleCellAssay.R
MAST/tests/testthat/test-SummarizedExperiment.R
MAST/tests/testthat/test-bootstrap.R
MAST/tests/testthat/test-convertMASTClassic.R
MAST/tests/testthat/test-helper-methods.R
MAST/tests/testthat/test-lmWrapper-bayesglm.R
MAST/tests/testthat/test-lmWrapper-glm.R
MAST/tests/testthat/test-lmWrapper-glmer.R
MAST/tests/testthat/test-lrtest.R
MAST/tests/testthat/test-thresholding.R
MAST/tests/testthat/test-zeroinf.R
MAST/tests/testthat/test-zlmfit.R
MAST/vignettes
MAST/vignettes/MAITAnalysis.Rmd
MAST/vignettes/MAST-intro.Rnw
MAST/vignettes/symbols.tex

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