Files in epurdom/clusterCells

Compare Clusterings for Single-Cell Sequencing

NotesOnKnn.md R/AllChecks.R R/AllClassesCE.R R/AllClassesCF.R R/AllGenerics.R R/AllHelper.R R/AllHelperClusterFunction.R R/AllHelperDendro.R R/AllHelperFilter.R R/JiashinJiCode.R R/RcppExports.R R/addClusterings.R R/assignUnassigned.R R/builtInClusterFunctions.R R/clusterContrasts.R R/clusterMany.R R/clusterSingle.R R/dataCreation.R R/deprecateFunctions.R R/getClusterIndex.R R/getFeatures.R R/getParams.R R/getReducedData.R R/internalClusterFunctions.R R/internalDendroFunctions.R R/internalFunctions.R R/mainClustering.R R/makeBlankData.R R/makeConsensus.R R/makeDendrogram.R R/makeFilterStats.R R/makeReducedDims.R R/mergeClusters.R R/plotBarplot.R R/plotClusters.R R/plotClustersTable.R R/plotClustersWorkflow.R R/plotContrastHeatmap.R R/plotDendrogram.R R/plotFeatureBoxplot.R R/plotFeatureScatter.R R/plotHeatmap.R R/plotReduceDim.R R/plottingHelpers.R R/rsec.R R/seqCluster.R R/subsampleClustering.R R/subsampleLoop.R R/subset.R R/transformFunction.R R/updateObject.R R/workflowClusters.R README.md longtests/testthat.R longtests/testthat/setup_create_objects.R longtests/testthat/test-rsec.R longtests/testthat/test-rsecFluidigm.R man/ClusterExperiment-class.Rd man/ClusterExperiment-methods.Rd man/ClusterFunction-class.Rd man/ClusterFunction-methods.Rd man/RSEC.Rd man/addClusterings.Rd man/assignUnassigned.Rd man/builtInClusteringFunctions.Rd man/clusterContrasts.Rd man/clusterDendrogram.Rd man/clusterExperiment-deprecated.Rd man/clusterMany.Rd man/clusterSingle.Rd man/fluidigmData.Rd man/getBestFeatures.Rd man/getClusterIndex.Rd man/getClusterManyParams.Rd man/mainClustering.Rd man/makeConsensus.Rd man/makeDendrogram.Rd man/mergeClusters.Rd man/numericalAsCharacter.Rd man/plotBarplot.Rd man/plotClusters.Rd man/plotClustersTable.Rd man/plotClustersWorkflow.Rd man/plotContrastHeatmap.Rd man/plotDendrogram.Rd man/plotFeatureBoxplot.Rd man/plotFeatureScatter.Rd man/plotHeatmap.Rd man/plotReducedDims.Rd man/plottingFunctions.Rd man/reduceFunctions.Rd man/renameClusters.Rd man/rsecFluidigm.Rd man/search_pairs.Rd man/seqCluster.Rd man/simData.Rd man/subsampleClustering.Rd man/subset.Rd man/transformData.Rd man/updateObject.Rd man/workflowClusters.Rd tests/checkClusterMany/check_subsample.R tests/checkClusterMany/clusterManyTest.R tests/checkClusterMany/clusterManyTestHDF5.R tests/checkClusterMany/makeData.R tests/checkClusterMany/oldmemTestDirectory/testLargeBig.R tests/checkClusterMany/oldmemTestDirectory/testLargeBig_subCore.R tests/checkClusterMany/oldmemTestDirectory/testLargeProfile_singleCore.R tests/checkClusterMany/oldmemTestDirectory/testLargeSmall.R tests/checkClusterMany/oldmemTestDirectory/testLargeSmall_subCore.R tests/checkClusterMany/oldmemTestDirectory/testStandardBig.R tests/checkClusterMany/oldmemTestDirectory/testStandardBig_subCore.R tests/checkClusterMany/oldmemTestDirectory/testStandardProfile_singleCore.R tests/checkClusterMany/oldmemTestDirectory/testStandardSmall.R tests/checkClusterMany/oldmemTestDirectory/testStandardSmall_subCore.R tests/checkClusterMany/readMemoryLog.R tests/testthat/setup_create_objects.R tests/testthat/test-ClusterFunction.R tests/testthat/test-RSEC.R tests/testthat/test-assays.R tests/testthat/test-clusterMany.R tests/testthat/test-clusterSingle.R tests/testthat/test-constructor.R tests/testthat/test-dendrogram.R tests/testthat/test-dimReduce.R tests/testthat/test-getBestFeatures.R tests/testthat/test-heatmaps.R tests/testthat/test-mainClustering.R tests/testthat/test-makeConsensus.R tests/testthat/test-mergeClusters.R tests/testthat/test-otherPlots.R tests/testthat/test-subsampleClustering.R tests/testthat_a-c.R tests/testthat_d-i.R tests/testthat_j-z.R tests/timeTests.R update2.0.md update2.4.md vignettes/clusterExperimentTutorial.Rmd vignettes/largeDataSets.Rmd