Files in RGLab/MAST
Model-based Analysis of Single Cell Transcriptomics

.github/.gitignore

.github/ISSUE_TEMPLATE/issue_template.md .github/ISSUE_TEMPLATE/usage_template.md

.gitignore

.travis.yml

DESCRIPTION

NAMESPACE

NEWS.md R/AllClasses.R R/AllGenerics.R R/CovFromBoots.R R/Fluidigm-methods.R R/GSEA-by-boot.R R/Hypothesis.R R/LmWrapper.R R/MAST-package.R R/MultidimensionalScaling.R R/RNASeqAssay-methods.R R/Readers.R R/SingleCellAssay-methods.R R/UtilityFunctions.R R/ZlmFit-bootstrap.R R/ZlmFit-logFC.R R/ZlmFit.R R/bayesglm.R R/convertMASTClassic.R R/ebayes-helpers.R R/filterEval.R R/helper-methods.R R/lmWrapper-bayesglm.R R/lmWrapper-glm.R R/lmWrapper-glmer.R R/lmWrapper-ridge.R R/lrtest.R R/predict.R R/stat_ell.R R/thresholdSCRNA.R R/zeroinf.R R/zlmHooks.R README.md

_pkgdown.yml

data/maits.RData

data/predicted_sig.RData

data/vbeta.RData

data/vbetaFA.RData

docs/404.html

docs/articles/MAITAnalysis.html

docs/articles/MAITAnalysis_cache/.gitignore

docs/articles/MAST-Intro.html

docs/articles/MAST-Intro_files/figure-html/advancedArmExample-1.png

docs/articles/MAST-Intro_files/figure-html/burdenOfFiltering-1.png

docs/articles/MAST-Intro_files/figure-html/splitbyncells-1.png

docs/articles/MAST-Intro_files/figure-html/tests-1.png

docs/articles/MAST-Intro_files/figure-html/zlmExample-1.png

docs/articles/MAST-interoperability.html

docs/articles/MAST-interoperability_files/figure-html/scaterQC-1.png

docs/articles/MAST-interoperability_files/figure-html/scaterQC-2.png

docs/articles/MAST-interoperability_files/figure-html/unnamed-chunk-1-1.png

docs/articles/MAST-interoperability_files/figure-html/unnamed-chunk-13-1.png

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docs/articles/MAST-interoperability_files/figure-html/unnamed-chunk-2-1.png

docs/articles/MAST-interoperability_files/figure-html/unnamed-chunk-9-1.png

docs/articles/MAST-intro.Rnw

docs/articles/MAST-intro.rel

docs/articles/figure/advancedArmExample-1.pdf docs/articles/figure/burdenOfFiltering-1.pdf docs/articles/figure/splitbyncells-1.pdf docs/articles/figure/tests-1.pdf docs/articles/figure/zlmExample-1.pdf

docs/articles/framed.sty

docs/articles/index.html

docs/articles/symbols.tex

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/BayesGLMlike-class.html

docs/reference/CovFromBoots.html

docs/reference/Drop.html

docs/reference/FromFlatDF.html

docs/reference/FromMatrix.html

docs/reference/GLMlike-class.html

docs/reference/GSEATests-class.html

docs/reference/Hypothesis.html

docs/reference/LMERlike-class.html

docs/reference/LMlike-class.html

docs/reference/LRT.html

docs/reference/MAST-defunct.html

docs/reference/MAST-package.html

docs/reference/Rplot001.png

docs/reference/Rplot002.png

docs/reference/SceToSingleCellAssay.html

docs/reference/ZlmFit-class.html

docs/reference/applyFlat.html

docs/reference/bootVcov1.html

docs/reference/cData.html

docs/reference/calcZ.html

docs/reference/colData-set-SingleCellAssay-DataFrame-method.html

docs/reference/collectResiduals.html

docs/reference/computeEtFromCt.html

docs/reference/condSd.html

docs/reference/condmean.html

docs/reference/convertMASTClassicToSingleCellAssay.html

docs/reference/defaultAssay.html

docs/reference/defaultPrior.html

docs/reference/dof.html

docs/reference/ebayes.html

docs/reference/expavg.html

docs/reference/fData-methods.html

docs/reference/featureData-methods.html

docs/reference/filter-4.png

docs/reference/filter-6.png

docs/reference/filter.html

docs/reference/filterLowExpressedGenes.html

docs/reference/fit.html

docs/reference/freq.html

docs/reference/getConcordance.html

docs/reference/getwellKey.html

docs/reference/gseaAfterBoot.html

docs/reference/hushWarning.html

docs/reference/impute-1.png

docs/reference/impute.html

docs/reference/index.html

docs/reference/influence.bayesglm.html

docs/reference/invlogit.html

docs/reference/logFC.html

docs/reference/logmean.html

docs/reference/lrTest-ZlmFit-character-method.html

docs/reference/lrTest.html

docs/reference/maits-dataset.html

docs/reference/mast_filter-1.png

docs/reference/mast_filter-2.png

docs/reference/mast_filter.html

docs/reference/meld_list_left.html

docs/reference/melt.SingleCellAssay.html

docs/reference/model.matrix-set.html

docs/reference/model.matrix.html

docs/reference/myBiplot.html

docs/reference/numexp.html

docs/reference/pbootVcov1.html

docs/reference/plot.thresholdSCRNACountMatrix-1.png

docs/reference/plot.thresholdSCRNACountMatrix.html

docs/reference/plotSCAConcordance-1.png

docs/reference/plotSCAConcordance-7.png

docs/reference/plotSCAConcordance.html

docs/reference/plotlrt.html

docs/reference/predict.ZlmFit-1.png

docs/reference/predict.ZlmFit.html

docs/reference/predicted_sig-dataset.html

docs/reference/primerAverage.html

docs/reference/print.summaryZlmFit.html

docs/reference/read.fluidigm.html

docs/reference/removeResponse.html

docs/reference/rstandard.bayesglm.html

docs/reference/se.coef.html

docs/reference/show.html

docs/reference/split-SingleCellAssay-character-method.html

docs/reference/stat_ell-1.png

docs/reference/stat_ell-6.png

docs/reference/stat_ell.html

docs/reference/subset-SingleCellAssay-method.html

docs/reference/summarize.html

docs/reference/summary-GSEATests-method.html

docs/reference/summary-ZlmFit-method.html

docs/reference/summary.thresholdSCRNACountMatrix.html

docs/reference/thresholdSCRNACountMatrix-1.png

docs/reference/thresholdSCRNACountMatrix-13.png

docs/reference/thresholdSCRNACountMatrix.html

docs/reference/vbeta-dataset.html

docs/reference/vbetaFA-dataset.html

docs/reference/waldTest-ZlmFit-matrix-method.html

docs/reference/waldTest.html

docs/reference/xform.html

docs/reference/zlm.SingleCellAssay.html

docs/reference/zlm.html

docs/sitemap.xml

inst/NEWS

inst/extdata/BTM_for_GSEA_20131008.gmt

man/BayesGLMlike-class.Rd man/CovFromBoots.Rd man/Drop.Rd man/FromFlatDF.Rd man/FromMatrix.Rd man/GLMlike-class.Rd man/GSEATests-class.Rd man/Hypothesis.Rd man/LMERlike-class.Rd man/LMlike-class.Rd man/LRT.Rd man/MAST-defunct.Rd man/MAST-package.Rd man/SceToSingleCellAssay.Rd man/ZlmFit-class.Rd man/applyFlat.Rd man/bootVcov1.Rd man/calcZ.Rd man/colData-set-SingleCellAssay-DataFrame-method.Rd man/collectResiduals.Rd man/computeEtFromCt.Rd man/convertMASTClassicToSingleCellAssay.Rd man/defaultAssay.Rd man/defaultPrior.Rd man/dof.Rd man/ebayes.Rd man/expavg.Rd man/filterLowExpressedGenes.Rd man/fit.Rd man/freq.Rd man/getConcordance.Rd man/getwellKey.Rd man/gseaAfterBoot.Rd man/hushWarning.Rd man/impute.Rd man/influence.bayesglm.Rd man/invlogit.Rd man/logFC.Rd man/logmean.Rd man/lrTest-ZlmFit-character-method.Rd man/lrTest.Rd man/maits-dataset.Rd man/mast_filter.Rd man/meld_list_left.Rd man/melt.SingleCellAssay.Rd man/model.matrix-set.Rd man/model.matrix.Rd man/myBiplot.Rd man/new_with_repaired_slots.Rd man/plot.thresholdSCRNACountMatrix.Rd man/plotSCAConcordance.Rd man/plotlrt.Rd man/predict.ZlmFit.Rd man/predicted_sig-dataset.Rd man/primerAverage.Rd man/print.summaryZlmFit.Rd man/read.fluidigm.Rd man/removeResponse.Rd man/rstandard.bayesglm.Rd man/se.coef.Rd man/show.Rd man/split-SingleCellAssay-character-method.Rd man/stat_ell.Rd man/subset-SingleCellAssay-method.Rd man/summarize.Rd man/summary-GSEATests-method.Rd man/summary-ZlmFit-method.Rd man/summary.thresholdSCRNACountMatrix.Rd man/thresholdSCRNACountMatrix.Rd man/vbeta-dataset.Rd man/vbetaFA-dataset.Rd man/waldTest-ZlmFit-matrix-method.Rd man/waldTest.Rd man/xform.Rd man/zlm.Rd tests/testthat.R

tests/testthat/SingleCellAssay-Object-MASTClassic.RData

vignettes/MAST-intro.tex

vignettes/mast-interopt.bib

vignettes/mastintro.bib

vignettes/symbols.tex

RGLab/MAST documentation built on Sept. 30, 2023, 1:08 p.m.

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RGLab/MAST
Model-based Analysis of Single Cell Transcriptomics

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Model-based Analysis of Single Cell Transcriptomics

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RGLab/MAST Model-based Analysis of Single Cell Transcriptomics

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RGLab/MAST
Model-based Analysis of Single Cell Transcriptomics

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Model-based Analysis of Single Cell Transcriptomics