Man pages for epurdom/clusterExperiment
Compare Clusterings for Single-Cell Sequencing
| addClusterings | Add clusterings to ClusterExperiment object |
| assignUnassigned | Assign unassigned samples to nearest cluster |
| builtInClusteringFunctions | Built in ClusterFunction options |
| clusterContrasts | Create contrasts for testing DE of a cluster |
| clusterDendrogram | Accessing and manipulating the dendrograms |
| ClusterExperiment-class | Class ClusterExperiment |
| clusterExperiment-deprecated | Deprecated functions in package 'clusterExperiment' |
| ClusterExperiment-methods | Helper methods for the ClusterExperiment class |
| ClusterFunction-class | Class ClusterFunction |
| ClusterFunction-methods | Helper methods for the ClusterFunction class |
| clusterMany | Create a matrix of clustering across values of parameters |
| clusterSingle | General wrapper method to cluster the data |
| fluidigmData | Subset of fluidigm data |
| getBestFeatures | Function for finding best features associated with clusters |
| getClusterIndex | getClusterIndex |
| getClusterManyParams | Get parameter values of clusterMany clusters |
| mainClustering | Cluster distance matrix from subsampling |
| makeConsensus | Find sets of samples that stay together across clusterings |
| makeDendrogram | Make hierarchy of set of clusters |
| mergeClusters | Merge clusters based on dendrogram |
| numericalAsCharacter | Convert numeric values to character that sort correctly |
| plotBarplot | Barplot of 1 or 2 clusterings |
| plotClusters | Visualize cluster assignments across multiple clusterings |
| plotClustersTable | Plot heatmap of cross-tabs of 2 clusterings |
| plotClustersWorkflow | A plot of clusterings specific for clusterMany and workflow... |
| plotContrastHeatmap | Plot heatmaps showing significant genes per contrast |
| plotDendrogram | Plot dendrogram of ClusterExperiment object |
| plotFeatureBoxplot | Plot boxplot of feature values by cluster |
| plotFeatureScatter | Plot scatter plot of feature values colored by cluster |
| plotHeatmap | Heatmap for showing clustering results and more |
| plotReducedDims | Plot 2-dimensionsal representation with clusters |
| plottingFunctions | Convert clusterLegend into useful formats |
| reduceFunctions | Return matrix from ClusterExperiment with reduced dimensions |
| renameClusters | Change assigned names or colors of clusters |
| RSEC | Resampling-based Sequential Ensemble Clustering |
| rsecFluidigm | Documentation of rsecFluidigm object |
| search_pairs | Search pairs of samples that co-cluster across subsamples |
| seqCluster | Program for sequentially clustering, removing cluster, and... |
| simData | Simulated data for running examples |
| subsampleClustering | Cluster subsamples of the data |
| subset | Functions to subset ClusterExperiment Objects |
| transformData | Transform the original data in a ClusterExperiment object |
| updateObject | Update old ClusterExperiment object to current class... |
| workflowClusters | Methods for workflow clusters |
