Files in splatter

Simple Simulation of Single-cell RNA Sequencing Data

README.md tests/testthat.R tests/spelling.R tests/testthat/test-PhenoParams.R tests/testthat/test-SimpleParams.R tests/testthat/test-utils.R tests/testthat/test-simpleEstimate.R tests/testthat/test-BASiCSParams.R tests/testthat/test-MFAParams.R tests/testthat/test-SCDDParams.R tests/testthat/test-simple-simulate.R tests/testthat/test-mfa-simulate.R tests/testthat/test-splatPopEstimate.R tests/testthat/test-lun2-simulate.R tests/testthat/test-SplatPopParams.R tests/testthat/test-Params.R tests/testthat/test-MFAEstimate.R tests/testthat/test-SparseDCParams.R tests/testthat/test-SCE-functions.R tests/testthat/test-LunParams.R tests/testthat/test-BASiCSEstimate.R tests/testthat/test-Lun2Params.R tests/testthat/test-lunEstimate.R tests/testthat/test-ZINBParams.R tests/testthat/test-BASiCS-simulate.R tests/testthat/test-pheno-simulate.R tests/testthat/test-listSims.R tests/testthat/test-sparseDCEstimate.R tests/testthat/test-splat-simulate.R tests/testthat/test-lun-simulate.R tests/testthat/test-SplatParams.R tests/testthat/test-scDD-simulate.R tests/testthat/test-kersplat-simulate.R tests/testthat/test-zinb-simulate.R tests/testthat/test-sparseDC-simulate.R tests/testthat/test-splatPop-simulate.R tests/testthat/test-phenoEstimate.R tests/testthat/test-compare.R R/mock-data.R R/sparseDC-simulate.R R/splat-simulate.R R/LunParams-methods.R R/Lun2Params-methods.R R/zinb-simulate.R R/PhenoParams-methods.R R/splat-estimate.R R/SCE-functions.R R/utils.R R/MFAParams-methods.R R/AllClasses.R R/mfa-estimate.R R/simple-simulate.R R/simple-estimate.R R/lun2-simulate.R R/BASiCS-estimate.R R/params-functions.R R/sparseDC-estimate.R R/SplatParams-methods.R R/scDD-estimate.R R/lun2-estimate.R R/SCDDParams-methods.R R/BASiCSParams-methods.R R/AllGenerics.R R/Params-methods.R R/kersplat-simulate.R R/zinb-estimate.R R/splatPop-simulate.R R/lun-simulate.R R/SimpleParams-methods.R R/pheno-estimate.R R/compare.R R/scDD-simulate.R R/lun-estimate.R R/KersplatParams-methods.R R/BASiCS-simulate.R R/SplatPopParams-methods.R R/ZINBParams-methods.R R/kersplat-estimate.R R/mfa-simulate.R R/splatPop-estimate.R R/splatter-package.R R/SparseDCParams-methods.R R/pheno-simulate.R R/listSims.R man/phenoSimulate.Rd man/splatPopeQTLEffects.Rd man/splatSimBCVMeans.Rd man/summariseDiff.Rd man/makeDiffPanel.Rd man/kersplatEstLib.Rd man/checkDependencies.Rd man/sparsifyMatrices.Rd man/logistic.Rd man/sparseDCEstimate.Rd man/bringItemsForward.Rd man/kersplatGenNetwork.Rd man/kersplatSample.Rd man/addFeatureStats.Rd man/lun2Estimate.Rd man/splatPopEstimateEffectSize.Rd man/splatSimBatchEffects.Rd man/splatPopQuantNormKey.Rd man/splatPopCleanSCE.Rd man/getParams.Rd man/splatPopSimulateSC.Rd man/setParamUnchecked.Rd man/splatPopSimMeans.Rd man/diffSCEs.Rd man/mfaSimulate.Rd man/simpleSimulate.Rd man/tidyStatSumm.Rd man/co.var.Rd man/mockBulkMatrix.Rd man/summariseKS.Rd man/splatPopParseVCF.Rd man/summariseStats.Rd man/splatEstLib.Rd man/addGeneLengths.Rd man/splatPopEstimate.Rd man/splatPopQuantNorm.Rd man/BASiCSSimulate.Rd man/getLNormFactors.Rd man/getParam.Rd man/getCounts.Rd man/compareSCEs.Rd man/ZINBParams.Rd man/SplatPopParams.Rd man/selectFit.Rd man/kersplatSimCellCounts.Rd man/splatSimTrueCounts.Rd man/minimiseSCE.Rd man/SplatParams.Rd man/splatSimulate.Rd man/kersplatSimLibSizes.Rd man/expandParams.Rd man/splatPopSimEffects.Rd man/setParam.Rd man/setParamsUnchecked.Rd man/lunEstimate.Rd man/PhenoParams.Rd man/kersplatSimPaths.Rd man/splatEstBCV.Rd man/lun2Simulate.Rd man/kersplatSetup.Rd man/mockVCF.Rd man/zinbSimulate.Rd man/kersplatSelectRegs.Rd man/splatPopAssignMeans.Rd man/showDFs.Rd man/makeCompPanel.Rd man/LunParams.Rd man/kersplatSimulate.Rd man/getPathOrder.Rd man/splatSimCellMeans.Rd man/splatEstimate.Rd man/SimpleParams.Rd man/showPP.Rd man/newParams.Rd man/rbindMatched.Rd man/splatPopSimulateMeans.Rd man/showValues.Rd man/bridge.Rd man/mockBulkeQTL.Rd man/scDDEstimate.Rd man/mfaEstimate.Rd man/kersplatEstBCV.Rd man/MFAParams.Rd man/splatEstMean.Rd man/splatPopSimulateSample.Rd man/splatPopSimulate.Rd man/splatSimBatchCellMeans.Rd man/splatter.Rd man/splatSimLibSizes.Rd man/kersplatSimAmbientCounts.Rd man/sparseDCSimulate.Rd man/sampleDensity.Rd man/BASiCSParams.Rd man/splatPopSimGeneMeans.Rd man/lunSimulate.Rd man/winsorize.Rd man/mockGFF.Rd man/splatSimGeneMeans.Rd man/simpleEstimate.Rd man/kersplatEstimate.Rd man/splatSimDE.Rd man/getBetaStepProbs.Rd man/kersplatSimGeneMeans.Rd man/splatPopParseGenes.Rd man/splatEstDropout.Rd man/listSims.Rd man/scDDSimulate.Rd man/kersplatEstMean.Rd man/kersplatSimCellMeans.Rd man/setParams.Rd man/BASiCSEstimate.Rd man/Lun2Params.Rd man/kersplatSimCounts.Rd man/KersplatParams.Rd man/makeOverallPanel.Rd man/Params.Rd man/zinbEstimate.Rd man/splatPopEstimateMeanCV.Rd man/splatEstOutlier.Rd man/SCDDParams.Rd man/splatPopGroupEffects.Rd man/splatSimDropout.Rd man/phenoEstimate.Rd man/SparseDCParams.Rd inst/doc/splatter.R inst/doc/splatPop.Rmd inst/doc/splat_params.Rmd inst/doc/splat_params.R inst/doc/splatPop.R inst/doc/splatter.Rmd vignettes/splatPop.Rmd vignettes/splat_params.Rmd vignettes/splatter.Rmd