Files in MAST
Model-based Analysis of Single Cell Transcriptomics

README.md
_pkgdown.yml
NAMESPACE
DESCRIPTION
NEWS
.travis.yml
tests/testthat.R tests/testthat/test-AllClasses.R tests/testthat/test-lmWrapper-glmer.R
tests/testthat/SingleCellAssay-Object-MASTClassic.RData
tests/testthat/test-convertMASTClassic.R tests/testthat/common-lmWrapper-tests.R tests/testthat/test-lmWrapper-glm.R tests/testthat/common-lmWrapper-glm-tests.R tests/testthat/test-lmWrapper-bayesglm.R tests/testthat/test-FluidigmAssay.R tests/testthat/test-thresholding.R tests/testthat/test-SummarizedExperiment.R tests/testthat/test-bootstrap.R tests/testthat/test-lrtest.R tests/testthat/test-zlmfit.R tests/testthat/test-Hypothesis.R tests/testthat/test-predict.R tests/testthat/test-zeroinf.R tests/testthat/helper-vbeta-init.R tests/testthat/test-SingleCellAssay.R tests/testthat/test-GSEA-by-boot.R tests/testthat/test-helper-methods.R
build/vignette.rds
inst/NEWS
inst/doc/MAST-Intro.R inst/doc/MAITAnalysis.Rmd
inst/doc/MAST-Intro.html
inst/doc/MAST-Intro.Rmd inst/doc/MAITAnalysis.R
inst/doc/MAITAnalysis.html
inst/extdata/BTM_for_GSEA_20131008.gmt
R/filterEval.R R/UtilityFunctions.R R/Readers.R R/zeroinf.R R/predict.R R/ebayes-helpers.R R/helper-methods.R R/Fluidigm-methods.R R/stat_ell.R R/convertMASTClassic.R R/LmWrapper.R R/MultidimensionalScaling.R R/lmWrapper-bayesglm.R R/Hypothesis.R R/ZlmFit-bootstrap.R R/AllGenerics.R R/RNASeqAssay-methods.R R/ZlmFit-logFC.R R/ZlmFit.R R/lmWrapper-glm.R R/zlmHooks.R R/AllClasses.R R/lmWrapper-ridge.R R/lmWrapper-glmer.R R/bayesglm.R R/SingleCellAssay-methods.R R/GSEA-by-boot.R R/lrtest.R R/thresholdSCRNA.R
docs/jquery.sticky-kit.min.js
docs/index.html
docs/pkgdown.css
docs/link.svg
docs/pkgdown.js
docs/authors.html
docs/articles/MAST-intro.rel
docs/articles/MAITAnalysis.html
docs/articles/MAST-intro.Rnw
docs/articles/framed.sty
docs/articles/index.html
docs/articles/symbols.tex
docs/articles/figure/tests-1.pdf docs/articles/figure/burdenOfFiltering-1.pdf docs/articles/figure/splitbyncells-1.pdf docs/articles/figure/zlmExample-1.pdf docs/articles/figure/advancedArmExample-1.pdf
docs/reference/gseaAfterBoot.html
docs/reference/split-SingleCellAssay-character-method.html
docs/reference/fData-methods.html
docs/reference/Drop.html
docs/reference/thresholdSCRNACountMatrix.html
docs/reference/show.html
docs/reference/print.summaryZlmFit.html
docs/reference/summary-ZlmFit-method.html
docs/reference/applyFlat.html
docs/reference/predict.ZlmFit.html
docs/reference/plotSCAConcordance-7.png
docs/reference/logmean.html
docs/reference/filter.html
docs/reference/logFC.html
docs/reference/vbetaFA-dataset.html
docs/reference/lrTest.html
docs/reference/zlm.html
docs/reference/plot.thresholdSCRNACountMatrix.html
docs/reference/subset-SingleCellAssay-method.html
docs/reference/collectResiduals.html
docs/reference/pbootVcov1.html
docs/reference/impute.html
docs/reference/maits-dataset.html
docs/reference/zlm.SingleCellAssay.html
docs/reference/removeResponse.html
docs/reference/MAST-package.html
docs/reference/filter-6.png
docs/reference/se.coef.html
docs/reference/featureData-methods.html
docs/reference/lrTest-ZlmFit-character-method.html
docs/reference/waldTest-ZlmFit-matrix-method.html
docs/reference/condSd.html
docs/reference/summary.thresholdSCRNACountMatrix.html
docs/reference/getConcordance.html
docs/reference/ZlmFit-class.html
docs/reference/waldTest.html
docs/reference/thresholdSCRNACountMatrix-13.png
docs/reference/stat_ell-6.png
docs/reference/computeEtFromCt.html
docs/reference/freq.html
docs/reference/LMERlike-class.html
docs/reference/condmean.html
docs/reference/xform.html
docs/reference/plotlrt.html
docs/reference/model.matrix-set.html
docs/reference/bootVcov1.html
docs/reference/numexp.html
docs/reference/dof.html
docs/reference/calcZ.html
docs/reference/BayesGLMlike-class.html
docs/reference/GLMlike-class.html
docs/reference/summary-GSEATests-method.html
docs/reference/plotSCAConcordance.html
docs/reference/vbeta-dataset.html
docs/reference/Hypothesis.html
docs/reference/stat_ell.html
docs/reference/index.html
docs/reference/FromMatrix.html
docs/reference/primerAverage.html
docs/reference/FromFlatDF.html
docs/reference/rstandard.bayesglm.html
docs/reference/summarize.html
docs/reference/invlogit.html
docs/reference/ebayes.html
docs/reference/getwellKey.html
docs/reference/myBiplot.html
docs/reference/filterLowExpressedGenes.html
docs/reference/hushWarning.html
docs/reference/cData.html
docs/reference/GSEATests-class.html
docs/reference/influence.bayesglm.html
docs/reference/read.fluidigm.html
docs/reference/fit.html
docs/reference/LRT.html
docs/reference/colData-set-SingleCellAssay-DataFrame-method.html
docs/reference/expavg.html
docs/reference/filter-4.png
docs/reference/defaultPrior.html
docs/reference/model.matrix.html
docs/reference/LMlike-class.html
docs/reference/convertMASTClassicToSingleCellAssay.html
docs/reference/melt.SingleCellAssay.html
man/computeEtFromCt.Rd man/applyFlat.Rd man/Drop.Rd man/myBiplot.Rd man/logmean.Rd man/predict.ZlmFit.Rd man/waldTest.Rd man/BayesGLMlike-class.Rd man/removeResponse.Rd man/GSEATests-class.Rd man/logFC.Rd man/freq.Rd man/split-SingleCellAssay-character-method.Rd man/GLMlike-class.Rd man/model.matrix.Rd man/plotlrt.Rd man/filterLowExpressedGenes.Rd man/show.Rd man/summary-ZlmFit-method.Rd man/bootVcov1.Rd man/hushWarning.Rd man/calcZ.Rd man/impute.Rd man/collectResiduals.Rd man/dof.Rd man/influence.bayesglm.Rd man/rstandard.bayesglm.Rd man/waldTest-ZlmFit-matrix-method.Rd man/MAST-package.Rd man/thresholdSCRNACountMatrix.Rd man/ebayes.Rd man/Hypothesis.Rd man/se.coef.Rd man/fData-methods.Rd man/pbootVcov1.Rd man/plotSCAConcordance.Rd man/LMERlike-class.Rd man/summary.thresholdSCRNACountMatrix.Rd man/lrTest-ZlmFit-character-method.Rd man/maits-dataset.Rd man/convertMASTClassicToSingleCellAssay.Rd man/defaultPrior.Rd man/stat_ell.Rd man/summarize.Rd man/fit.Rd man/LRT.Rd man/vbeta-dataset.Rd man/model.matrix-set.Rd man/print.summaryZlmFit.Rd man/read.fluidigm.Rd man/expavg.Rd man/zlm.Rd man/FromMatrix.Rd man/plot.thresholdSCRNACountMatrix.Rd man/xform.Rd man/summary-GSEATests-method.Rd man/primerAverage.Rd man/featureData-methods.Rd man/FromFlatDF.Rd man/melt.SingleCellAssay.Rd man/cData.Rd man/gseaAfterBoot.Rd man/vbetaFA-dataset.Rd man/getConcordance.Rd man/colData-set-SingleCellAssay-DataFrame-method.Rd man/mast_filter.Rd man/LMlike-class.Rd man/getwellKey.Rd man/invlogit.Rd man/lrTest.Rd man/subset-SingleCellAssay-method.Rd man/ZlmFit-class.Rd vignettes/MAITAnalysis.Rmd vignettes/MAST-Intro.Rmd
vignettes/mastintro.bib
vignettes/symbols.tex
data/vbeta.RData
data/vbetaFA.RData
data/datalist
data/maits.RData
MAST documentation built on Nov. 17, 2017, 1:28 p.m.