Files in epurdom/clusterCells
Compare Clusterings for Single-Cell Sequencing
.BBSoptions
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
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
appveyor.yml
data/fluidigmColData.rda
data/fluidigmData.rda
data/rsecFluidigm.rda
data/simData.rda
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
src/.gitignore
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/search_pairs.cpp
src/subsampleLoop.cpp
tests/checkClusterMany/check_subsample.R
tests/checkClusterMany/clusterManyTest.R
tests/checkClusterMany/clusterManyTestHDF5.R
tests/checkClusterMany/fixedClusterManyResult.txt
tests/checkClusterMany/makeData.R
tests/checkClusterMany/oldmemTestDirectory/testLargeBig.R
tests/checkClusterMany/oldmemTestDirectory/testLargeBig.sh
tests/checkClusterMany/oldmemTestDirectory/testLargeBig_subCore.R
tests/checkClusterMany/oldmemTestDirectory/testLargeBig_subCore.sh
tests/checkClusterMany/oldmemTestDirectory/testLargeProfile_singleCore.R
tests/checkClusterMany/oldmemTestDirectory/testLargeProfile_singleCore.sh
tests/checkClusterMany/oldmemTestDirectory/testLargeSmall.R
tests/checkClusterMany/oldmemTestDirectory/testLargeSmall.sh
tests/checkClusterMany/oldmemTestDirectory/testLargeSmall_singleCore.sh
tests/checkClusterMany/oldmemTestDirectory/testLargeSmall_subCore.R
tests/checkClusterMany/oldmemTestDirectory/testLargeSmall_subCore.sh
tests/checkClusterMany/oldmemTestDirectory/testStandardBig.R
tests/checkClusterMany/oldmemTestDirectory/testStandardBig.sh
tests/checkClusterMany/oldmemTestDirectory/testStandardBig_subCore.R
tests/checkClusterMany/oldmemTestDirectory/testStandardBig_subCore.sh
tests/checkClusterMany/oldmemTestDirectory/testStandardProfile_singleCore.R
tests/checkClusterMany/oldmemTestDirectory/testStandardProfile_singleCore.sh
tests/checkClusterMany/oldmemTestDirectory/testStandardSmall.R
tests/checkClusterMany/oldmemTestDirectory/testStandardSmall.sh
tests/checkClusterMany/oldmemTestDirectory/testStandardSmall_subCore.R
tests/checkClusterMany/oldmemTestDirectory/testStandardSmall_subCore.sh
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
todoForKNN.txt
update2.0.md
update2.4.md
vignettes/bibFile.bib
vignettes/clusterExperimentTutorial.Rmd
vignettes/largeDataSets.Rmd
