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A B C D F G I L M N O P R S T W misc
| addClusterings | Functions to add/remove clusters to ClusterExperiment |
| addClusterings-method | Functions to add/remove clusters to ClusterExperiment |
| algorithmType | Helper methods for the ClusterFunction class |
| algorithmType-method | Helper methods for the ClusterFunction class |
| bigPalette | Convert clusterLegend into useful formats |
| clusterContrasts | Create contrasts for testing DE of a cluster |
| clusterContrasts-method | Create contrasts for testing DE of a cluster |
| ClusterExperiment | Class ClusterExperiment |
| ClusterExperiment-class | Class ClusterExperiment |
| ClusterExperiment-method | Class ClusterExperiment |
| ClusterExperiment-methods | Helper methods for the ClusterExperiment class |
| ClusterFunction | Class ClusterFunction |
| ClusterFunction-class | Class ClusterFunction |
| ClusterFunction-method | Class ClusterFunction |
| ClusterFunction-methods | Helper methods for the ClusterFunction class |
| clusteringInfo | Helper methods for the ClusterExperiment class |
| clusteringInfo-method | Helper methods for the ClusterExperiment class |
| clusterLabels | Helper methods for the ClusterExperiment class |
| clusterLabels-method | Helper methods for the ClusterExperiment class |
| clusterLabels<- | Helper methods for the ClusterExperiment class |
| clusterLabels<--method | Helper methods for the ClusterExperiment class |
| clusterLegend | Helper methods for the ClusterExperiment class |
| clusterLegend-method | Helper methods for the ClusterExperiment class |
| clusterLegend<- | Helper methods for the ClusterExperiment class |
| clusterLegend<--method | Helper methods for the ClusterExperiment class |
| clusterMany | Create a matrix of clustering across values of parameters |
| clusterMany-method | Create a matrix of clustering across values of parameters |
| clusterMatrix | Helper methods for the ClusterExperiment class |
| clusterMatrix-method | Helper methods for the ClusterExperiment class |
| clusterMatrixNamed | Helper methods for the ClusterExperiment class |
| clusterMatrixNamed-method | Helper methods for the ClusterExperiment class |
| clusterSingle | General wrapper method to cluster the data |
| clusterSingle-method | General wrapper method to cluster the data |
| clusterTypes | Helper methods for the ClusterExperiment class |
| clusterTypes-method | Helper methods for the ClusterExperiment class |
| clusterTypes<- | Helper methods for the ClusterExperiment class |
| clusterTypes<--method | Helper methods for the ClusterExperiment class |
| coClustering | Helper methods for the ClusterExperiment class |
| coClustering-method | Helper methods for the ClusterExperiment class |
| coClustering<- | Helper methods for the ClusterExperiment class |
| coClustering<--method | Helper methods for the ClusterExperiment class |
| combineMany | Find sets of samples that stay together across clusterings |
| combineMany-method | Find sets of samples that stay together across clusterings |
| convertClusterLegend | Convert clusterLegend into useful formats |
| convertClusterLegend-method | Convert clusterLegend into useful formats |
| defaultNDims | Filtering statistics and Dimensionality Reduction Functions |
| defaultNDims-method | Filtering statistics and Dimensionality Reduction Functions |
| dendroClusterIndex | Helper methods for the ClusterExperiment class |
| dendroClusterIndex-method | Helper methods for the ClusterExperiment class |
| filterData | Filtering statistics and Dimensionality Reduction Functions |
| filterData-method | Filtering statistics and Dimensionality Reduction Functions |
| filterNames | Filtering statistics and Dimensionality Reduction Functions |
| filterNames-method | Filtering statistics and Dimensionality Reduction Functions |
| getBestFeatures | Function for finding best features associated with clusters |
| getBestFeatures-method | Function for finding best features associated with clusters |
| getBuiltInFunction | Built in ClusterFunction options |
| getBuiltInFunction-method | Built in ClusterFunction options |
| getClusterManyParams | Get parameter values of clusterMany clusters |
| getClusterManyParams-method | Get parameter values of clusterMany clusters |
| getMergeCorrespond | Merge clusters based on dendrogram |
| getMergeCorrespond-method | Merge clusters based on dendrogram |
| getPostProcessingArgs | Cluster distance matrix from subsampling |
| getPostProcessingArgs-method | Cluster distance matrix from subsampling |
| inputType | Helper methods for the ClusterFunction class |
| inputType-method | Helper methods for the ClusterFunction class |
| internalFunctionCheck | Class ClusterFunction |
| listBuiltInFilterStats | Filtering statistics and Dimensionality Reduction Functions |
| listBuiltInFunctions | Built in ClusterFunction options |
| listBuiltInReducedDims | Filtering statistics and Dimensionality Reduction Functions |
| listBuiltInType01 | Built in ClusterFunction options |
| listBuiltInTypeK | Built in ClusterFunction options |
| mainClustering | Cluster distance matrix from subsampling |
| mainClustering-method | Cluster distance matrix from subsampling |
| makeBlankData | Convert clusterLegend into useful formats |
| makeDendrogram | Make hierarchy of set of clusters |
| makeDendrogram-method | Make hierarchy of set of clusters |
| makeFilterStats | Filtering statistics and Dimensionality Reduction Functions |
| makeFilterStats-method | Filtering statistics and Dimensionality Reduction Functions |
| makeReducedDims | Filtering statistics and Dimensionality Reduction Functions |
| makeReducedDims-method | Filtering statistics and Dimensionality Reduction Functions |
| massivePalette | Convert clusterLegend into useful formats |
| mergeClusterIndex | Merge clusters based on dendrogram |
| mergeClusterIndex-method | Merge clusters based on dendrogram |
| mergeClusters | Merge clusters based on dendrogram |
| mergeClusters-method | Merge clusters based on dendrogram |
| mergeCutoff | Merge clusters based on dendrogram |
| mergeCutoff-method | Merge clusters based on dendrogram |
| mergeMethod | Merge clusters based on dendrogram |
| mergeMethod-method | Merge clusters based on dendrogram |
| nClusterings | Helper methods for the ClusterExperiment class |
| nClusterings-method | Helper methods for the ClusterExperiment class |
| nClusters | Helper methods for the ClusterExperiment class |
| nClusters-method | Helper methods for the ClusterExperiment class |
| nFeatures | Helper methods for the ClusterExperiment class |
| nFeatures-method | Helper methods for the ClusterExperiment class |
| nodeMergeInfo | Merge clusters based on dendrogram |
| nodeMergeInfo-method | Merge clusters based on dendrogram |
| nSamples | Helper methods for the ClusterExperiment class |
| nSamples-method | Helper methods for the ClusterExperiment class |
| orderSamples | Helper methods for the ClusterExperiment class |
| orderSamples-method | Helper methods for the ClusterExperiment class |
| orderSamples<- | Helper methods for the ClusterExperiment class |
| orderSamples<--method | Helper methods for the ClusterExperiment class |
| plotBarplot | Barplot of 1 or 2 clusterings |
| plotBarplot-method | Barplot of 1 or 2 clusterings |
| plotClusterLegend | Convert clusterLegend into useful formats |
| plotClusterLegend-method | Convert clusterLegend into useful formats |
| plotClusters | Visualize cluster assignments across multiple clusterings |
| plotClusters-method | Visualize cluster assignments across multiple clusterings |
| plotClustersWorkflow | A plot of clusterings specific for clusterMany and workflow visualization |
| plotClustersWorkflow-method | A plot of clusterings specific for clusterMany and workflow visualization |
| plotCoClustering | Heatmap for showing clustering results and more |
| plotCoClustering-method | Heatmap for showing clustering results and more |
| plotContrastHeatmap | Plot heatmaps showing significant genes per contrast |
| plotContrastHeatmap-method | Plot heatmaps showing significant genes per contrast |
| plotDendrogram | Plot dendrogram of ClusterExperiment object |
| plotDendrogram-method | Plot dendrogram of ClusterExperiment object |
| plotFeatureBoxplot | Plot boxplot of feature values by cluster |
| plotFeatureBoxplot-method | Plot boxplot of feature values by cluster |
| plotHeatmap | Heatmap for showing clustering results and more |
| plotHeatmap-method | Heatmap for showing clustering results and more |
| plotReducedDims | Plot 2-dimensionsal representation with clusters |
| plotReducedDims-method | Plot 2-dimensionsal representation with clusters |
| plottingFunctions | Convert clusterLegend into useful formats |
| primaryCluster | Helper methods for the ClusterExperiment class |
| primaryCluster-method | Helper methods for the ClusterExperiment class |
| primaryClusterIndex | Helper methods for the ClusterExperiment class |
| primaryClusterIndex-method | Helper methods for the ClusterExperiment class |
| primaryClusterIndex<- | Helper methods for the ClusterExperiment class |
| primaryClusterIndex<--method | Helper methods for the ClusterExperiment class |
| primaryClusterNamed | Helper methods for the ClusterExperiment class |
| primaryClusterNamed-method | Helper methods for the ClusterExperiment class |
| reduceFunctions | Filtering statistics and Dimensionality Reduction Functions |
| removeClusterings | Functions to add/remove clusters to ClusterExperiment |
| removeClusterings-method | Functions to add/remove clusters to ClusterExperiment |
| removeClusters | Functions to add/remove clusters to ClusterExperiment |
| removeClusters-method | Functions to add/remove clusters to ClusterExperiment |
| removeUnclustered | Functions to add/remove clusters to ClusterExperiment |
| removeUnclustered-method | Functions to add/remove clusters to ClusterExperiment |
| requiredArgs | Helper methods for the ClusterFunction class |
| requiredArgs-method | Helper methods for the ClusterFunction class |
| RSEC | Resampling-based Sequential Ensemble Clustering |
| RSEC-method | Resampling-based Sequential Ensemble Clustering |
| RSEC-methods | Resampling-based Sequential Ensemble Clustering |
| rsecFluidigm | RSEC run for vignette |
| search_pairs | Search pairs of samples that co-cluster across subsamples |
| seqCluster | Program for sequentially clustering, removing cluster, and starting again. |
| seqPal1 | Convert clusterLegend into useful formats |
| seqPal2 | Convert clusterLegend into useful formats |
| seqPal3 | Convert clusterLegend into useful formats |
| seqPal4 | Convert clusterLegend into useful formats |
| seqPal5 | Convert clusterLegend into useful formats |
| setBreaks | Convert clusterLegend into useful formats |
| setToCurrent | Methods for workflow clusters |
| setToCurrent-method | Methods for workflow clusters |
| setToFinal | Methods for workflow clusters |
| setToFinal-method | Methods for workflow clusters |
| show-method | Helper methods for the ClusterExperiment class |
| showHeatmapPalettes | Convert clusterLegend into useful formats |
| showPalette | Convert clusterLegend into useful formats |
| simCount | Simulated data for running examples |
| simData | Simulated data for running examples |
| subsampleClustering | Cluster subsamples of the data |
| subsampleClustering-method | Cluster subsamples of the data |
| tableClusters | Helper methods for the ClusterExperiment class |
| tableClusters-method | Helper methods for the ClusterExperiment class |
| transformation | Helper methods for the ClusterExperiment class |
| transformation-method | Helper methods for the ClusterExperiment class |
| transformation<- | Helper methods for the ClusterExperiment class |
| transformation<--method | Helper methods for the ClusterExperiment class |
| transformData | Transform the original data in a ClusterExperiment object |
| transformData-method | Transform the original data in a ClusterExperiment object |
| trueCluster | Simulated data for running examples |
| workflowClusterDetails | Methods for workflow clusters |
| workflowClusterDetails-method | Methods for workflow clusters |
| workflowClusters | Methods for workflow clusters |
| workflowClusters-method | Methods for workflow clusters |
| workflowClusterTable | Methods for workflow clusters |
| workflowClusterTable-method | Methods for workflow clusters |
| [-method | Helper methods for the ClusterExperiment class |