API for davnovak/SingleBench
Framework for benchmarking and optimising dimension-reduction and clustering pipelines in expression data analysis
| Global functions | |
|---|---|
| .AddLayout.ValidityChecks | Source code |
| .AlignSubpipelines.ValidityChecks | Source code |
| .Benchmark.ValidityChecks | Source code |
| .Chain.ValidityChecks | Source code |
| .Fix.ValidityChecks | Source code |
| .JaccardSimilarityHeatmap | Source code |
| .Module.ValidityChecks | Source code |
| .Plot.ValidityChecks | Source code |
| .PlotClustering.ValidityChecks | Source code |
| .PlotJaccardHeatmap.ValidityChecks | Source code |
| .PlotProjection.ValidityChecks | Source code |
| .Subpipeline.ValidityChecks | Source code |
| .WhatIs.ValidityChecks | Source code |
| .WrapTool.ValidityChecks | Source code |
| .h5_slotname | Source code |
| .h5read | Source code |
| .h5readAnnotationScoring | Source code |
| .h5readClusterMedians | Source code |
| .h5readClusteringInput | Source code |
| .h5readClusteringResult | Source code |
| .h5readClusteringScoring | Source code |
| .h5readDistanceMatrix | Source code |
| .h5readFactorVectorOrListOfThem | Source code |
| .h5readLabelMedians | Source code |
| .h5readNamedMatrix | Source code |
| .h5readProjectionResult | Source code |
| .h5readProjectionScoring | Source code |
| .h5readkNNMatrix | Source code |
| .h5write | Source code |
| .h5writeAnnotationScoring | Source code |
| .h5writeClusterMedians | Source code |
| .h5writeClusteringIntermediate | Source code |
| .h5writeClusteringResult | Source code |
| .h5writeClusteringScoring | Source code |
| .h5writeDistanceMatrix | Source code |
| .h5writeFactorVectorOrListOfThem | Source code |
| .h5writeLabelMedians | Source code |
| .h5writeNamedMatrix | Source code |
| .h5writeProjectionIntermediate | Source code |
| .h5writeProjectionReference | Source code |
| .h5writeProjectionResult | Source code |
| .h5writeProjectionScoring | Source code |
| .h5writekNNMatrix | Source code |
| .msg | Source code |
| .msg_alt | Source code |
| .msg_alt_bad | Source code |
| .msg_alt_good | Source code |
| .msg_hpc | Source code |
| .msg_lite | Source code |
| .msg_name | Source code |
| .msg_python | Source code |
| .msg_val | Source code |
| .onAttach | Source code |
| AddLayout | Man page Source code |
| AddLayout.Benchmark | Source code |
| AlignChannelMarkerPairsNames | Source code |
| AlignSubpipelines | Source code |
| Benchmark | Man page Source code |
| BijectiveMatch | Source code |
| Chain | Source code |
| CloneClusteringTool | Source code |
| CloneFrom | Man page Source code |
| CloneProjectionTool | Source code |
| CollapsedCorankingMatrix | Source code |
| ComputekNNMatrix | Man page Source code |
| CreatePenaltyScoringMatrix | Man page Source code |
| DeployClustering_Bootstrap | Source code |
| DeployClustering_Repeat | Source code |
| DeployClustering_SingleRun | Source code |
| DeployProjection | Source code |
| EvalClustering | Source code |
| EvalProjection | Source code |
| Evaluate | Man page Source code |
| Evaluate.Benchmark | Source code |
| Evaluate_ComputekNNMatrix | Source code |
| ExtendGates | Man page Source code |
| FindProjectionResultIfAlreadyGenerated | Source code |
| Fix | Man page Source code |
| GatherInput | Source code |
| GatherInput_FCSPaths | Source code |
| GatherInput_SummarizedExperiment | Source code |
| GatherInput_flowSet | Source code |
| GetAnnotation | Man page Source code |
| GetAnnotationScoring | Man page Source code |
| GetBootstrapIndices | Man page Source code |
| GetChannelsAndMarkers | Man page Source code |
| GetClusterSizes | Source code |
| GetClustering | Man page Source code |
| GetClusteringInput | Man page Source code |
| GetClusteringModuleCount | Source code |
| GetClusteringScores | Man page Source code |
| GetClusteringScoringTable | Man page Source code |
| GetCoRanking | Man page Source code |
| GetDistanceMatrix | Man page Source code |
| GetExpressionMatrix | Man page Source code |
| GetLabelClusterMatching | Source code |
| GetLayout | Man page Source code |
| GetMatchedClusterSizes | Source code |
| GetNParameterIterationName | Man page Source code |
| GetNParameterIterationName_Clustering | Man page Source code |
| GetNParameterIterationName_Projection | Man page Source code |
| GetNParameterIterationsCount | Man page Source code |
| GetNParameterNames | Man page Source code |
| GetNParameterValues | Man page Source code |
| GetPenaltyScoringMatrix | Man page Source code |
| GetPopulationSizes | Source code |
| GetProjection | Man page Source code |
| GetProjectionModuleCount | Source code |
| GetProjectionScores | Man page Source code |
| GetProjectionScoringTable | Man page Source code |
| GetRMSDPerCluster | Man page Source code |
| GetRMSDPerPopulation | Source code |
| GetScores | Man page Source code |
| GetSubpipelineName | Man page Source code |
| GetSubpipelineTags | Source code |
| GetkNNMatrix | Man page Source code |
| HDF5_CreateHDF5AndWriteInputs | Source code |
| HDF5_InitialiseEvaluationResults | Source code |
| IsClone | Source code |
| IsClusteringWrapper | Source code |
| IsFormat | Source code |
| IsListOfClusteringWrappers | Source code |
| IsListOfProjectionWrappers | Source code |
| IsNonwrapper | Source code |
| IsProjectionWrapper | Source code |
| IsWrapper | Source code |
| Jacc | Man page Source code |
| JaccardTable | Source code |
| LoadWrappers | Man page Source code |
| MergeOverlaps | Source code |
| Module | Man page Source code |
| NameIsLegal | Source code |
| PlotClusterHeatmap | Man page Source code |
| PlotClustersOverlay | Man page Source code |
| PlotCoRanking | Man page Source code |
| PlotCollapsedCorankingMatrix | Source code |
| PlotCompositionMap | Man page Source code |
| PlotFullCorankingMatrix | Source code |
| PlotJaccardHeatmap | Source code |
| PlotLabelsOverlay | Man page Source code |
| PlotNParameterMap_Clustering | Man page Source code |
| PlotPopulationHeatmap | Man page Source code |
| PlotRMSDToSize | Man page Source code |
| PlotSimilarityHeatmap | Man page |
| PrintNParams | Source code |
| RelaxedMatch | Source code |
| ResolveFeatureIndices | Source code |
| SaveDistanceMatrix | Source code |
| SavePenaltyScoringMatrix | Source code |
| SavekNNMatrix | Source code |
| ScoreAnnotation | Man page Source code |
| ScoreClustering | Man page Source code |
| ScoreProjection | Source code |
| SeparateIntoSamples | Source code |
| ShortenPath | Source code |
| ShowReadout_Clustering | Man page Source code |
| ShowReadout_Projection | Man page Source code |
| SimplifyPath | Source code |
| Subpipeline | Man page Source code |
| TryWritePermission | Source code |
| WhatIs | Man page Source code |
| WrapTool | Man page Source code |
| ari | Source code |
| denoise_matrix | Source code |
| fExtract.Module | Source code |
| fExtract.ModuleChain | Source code |
| fExtract.WrapperWithParameters | Source code |
| fMap.Module | Source code |
| fMap.ModuleChain | Source code |
| fMap.WrapperWithParameters | Source code |
| fTrain.Module | Source code |
| fTrain.ModuleChain | Source code |
| fTrain.WrapperWithParameters | Source code |
| kNNGTweak | Man page Source code |
| knn_annoy | Source code |
| pSmoothSingleIter | Source code |
| penalty | Source code |
| print.Benchmark | Source code |
| print.Clone | Source code |
| print.Module | Source code |
| print.ModuleChain | Source code |
| print.Subpipeline | Source code |
| print.WrapperWithParameters | Source code |
| rmsd_per_cluster | Source code |
