Files in davnovak/SingleBench

Framework for benchmarking and optimising dimension-reduction and clustering pipelines in expression data analysis

R/00_Wrappers.R R/01_AlignChannels.R R/01_BenchmarkSetUp_.R R/01_BenchmarkSetUp_00_Modules.R R/01_BenchmarkSetUp_01_GatherData.R R/01_BenchmarkSetUp_02_Print.R R/02_Evaluate_.R R/02_Evaluate_Clustering_.R R/02_Evaluate_Clustering_01_SingleRun.R R/02_Evaluate_Clustering_02_Repeat.R R/02_Evaluate_Clustering_03_Bootstrap.R R/02_Evaluate_Projection.R R/02_Evaluate_kNN.R R/02_Layout.R R/03_Scoring_Annotation_.R R/03_Scoring_Clustering_.R R/03_Scoring_Clustering_00_Unsupervised.R R/03_Scoring_Clustering_01_JaccardTable.R R/03_Scoring_Clustering_02_Matching.R R/03_Scoring_Projection_.R R/04_Visual_CoRanking.R R/04_Visual_CompositionMaps.R R/04_Visual_Heatmaps.R R/04_Visual_JaccardHeatmap.R R/04_Visual_NParamMap.R R/04_Visual_Overlays.R R/04_Visual_RMSDToSize.R R/04_Visual_Readouts.R R/99_ClusterFeatures.R R/99_ConsoleTools.R R/99_Getters.R R/99_HDF5_01_Helpers.R R/99_HDF5_02_Initialise.R R/99_HierarchicalPenalties.R R/99_IOHelpers.R R/99_Jacc.R R/99_ProjectionRecycling.R R/99_ValidityChecks.R R/99_WhatIs.R R/99_kNNGating.R R/RcppExports.R R/zzz.R README.md inst/extdata/load_wrappers.R inst/extdata/wrappers_clustering/ClusterX.R inst/extdata/wrappers_clustering/Depeche.R inst/extdata/wrappers_clustering/FlowGrid.R inst/extdata/wrappers_clustering/FlowSOM.R inst/extdata/wrappers_clustering/PAC.R inst/extdata/wrappers_clustering/Phenograph.R inst/extdata/wrappers_clustering/SamSPECTRAL.R inst/extdata/wrappers_clustering/cytometree.R inst/extdata/wrappers_clustering/densitycut.R inst/extdata/wrappers_clustering/flowMeans.R inst/extdata/wrappers_clustering/flowPeaks.R inst/extdata/wrappers_clustering/immunoClust.R inst/extdata/wrappers_clustering/kmeans.R inst/extdata/wrappers_projection/DiffusionMap.R inst/extdata/wrappers_projection/EmbedSOM.R inst/extdata/wrappers_projection/PCA.R inst/extdata/wrappers_projection/Smooth.R inst/extdata/wrappers_projection/UMAP.R inst/extdata/wrappers_projection/VAE.R inst/extdata/wrappers_projection/ivis.R inst/extdata/wrappers_projection/pSmooth.R inst/extdata/wrappers_projection/tSNE.R man/AddLayout.Rd man/Benchmark.Rd man/CloneFrom.Rd man/ComputekNNMatrix.Rd man/CreatePenaltyScoringMatrix.Rd man/Evaluate.Rd man/ExtendGates.Rd man/Fix.Rd man/GetAnnotation.Rd man/GetAnnotationScoring.Rd man/GetBootstrapIndices.Rd man/GetChannelsAndMarkers.Rd man/GetClustering.Rd man/GetClusteringInput.Rd man/GetClusteringScores.Rd man/GetClusteringScoringTable.Rd man/GetCoRanking.Rd man/GetDistanceMatrix.Rd man/GetExpressionMatrix.Rd man/GetLayout.Rd man/GetNParameterIterationName.Rd man/GetNParameterIterationName_Clustering.Rd man/GetNParameterIterationName_Projection.Rd man/GetNParameterIterationsCount.Rd man/GetNParameterNames.Rd man/GetNParameterValues.Rd man/GetPenaltyScoringMatrix.Rd man/GetProjection.Rd man/GetProjectionScores.Rd man/GetProjectionScoringTable.Rd man/GetRMSDPerCluster.Rd man/GetScores.Rd man/GetSubpipelineName.Rd man/GetkNNMatrix.Rd man/Jacc.Rd man/LoadWrappers.Rd man/Module.Rd man/PlotClusterHeatmap.Rd man/PlotClustersOverlay.Rd man/PlotCoRanking.Rd man/PlotCompositionMap.Rd man/PlotLabelsOverlay.Rd man/PlotNParameterMap_Clustering.Rd man/PlotPopulationHeatmap.Rd man/PlotRMSDToSize.Rd man/PlotSimilarityHeatmap.Rd man/ScoreAnnotation.Rd man/ScoreClustering.Rd man/ShowReadout_Clustering.Rd man/ShowReadout_Projection.Rd man/Subpipeline.Rd man/WhatIs.Rd man/WrapTool.Rd man/kNNGTweak.Rd