Man pages for clusterExperiment
Compare Clusterings for Single-Cell Sequencing

addClusteringsAdd clusterings to ClusterExperiment object
assignUnassignedAssign unassigned samples to nearest cluster
builtInClusteringFunctionsBuilt in ClusterFunction options
clusterContrastsCreate contrasts for testing DE of a cluster
clusterDendrogramAccessing and manipulating the dendrograms
ClusterExperiment-classClass ClusterExperiment
clusterExperiment-deprecatedDeprecated functions in package 'clusterExperiment'
ClusterExperiment-methodsHelper methods for the ClusterExperiment class
ClusterFunction-classClass ClusterFunction
ClusterFunction-methodsHelper methods for the ClusterFunction class
clusterManyCreate a matrix of clustering across values of parameters
clusterSingleGeneral wrapper method to cluster the data
fluidigmDataSubset of fluidigm data
getBestFeaturesFunction for finding best features associated with clusters
getClusterManyParamsGet parameter values of clusterMany clusters
mainClusteringCluster distance matrix from subsampling
makeConsensusFind sets of samples that stay together across clusterings
makeDendrogramMake hierarchy of set of clusters
mergeClustersMerge clusters based on dendrogram
numericalAsCharacterConvert numeric values to character that sort correctly
plotBarplotBarplot of 1 or 2 clusterings
plotClustersVisualize cluster assignments across multiple clusterings
plotClustersTablePlot heatmap of cross-tabs of 2 clusterings
plotClustersWorkflowA plot of clusterings specific for clusterMany and workflow...
plotContrastHeatmapPlot heatmaps showing significant genes per contrast
plotDendrogramPlot dendrogram of ClusterExperiment object
plotFeatureBoxplotPlot boxplot of feature values by cluster
plotFeatureScatterPlot scatter plot of feature values colored by cluster
plotHeatmapHeatmap for showing clustering results and more
plotReducedDimsPlot 2-dimensionsal representation with clusters
plottingFunctionsConvert clusterLegend into useful formats
reduceFunctionsReturn matrix from ClusterExperiment with reduced dimensions
renameClustersChange assigned names or colors of clusters
RSECResampling-based Sequential Ensemble Clustering
rsecFluidigmDocumentation of rsecFluidigm object
search_pairsSearch pairs of samples that co-cluster across subsamples
seqClusterProgram for sequentially clustering, removing cluster, and...
simDataSimulated data for running examples
subsampleClusteringCluster subsamples of the data
subsetFunctions to subset ClusterExperiment Objects
transformDataTransform the original data in a ClusterExperiment object
updateObjectUpdate old ClusterExperiment object to current class...
workflowClustersMethods for workflow clusters
clusterExperiment documentation built on Feb. 11, 2021, 2 a.m.