clusterExperiment
Compare Clusterings for Single-Cell Sequencing

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clusterExperiment: Compare Clusterings for Single-Cell Sequencing
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API for clusterExperiment
Compare Clusterings for Single-Cell Sequencing

Global functions
.addBackSEInfo Source code
.addNewResult Source code
.addPrefixToClusterNames Source code
.addTreesToTips Source code
.checkArgs Source code
.checkAssays Source code
.checkCFInput Source code
.checkClusterLabels Source code
.checkClusterLegend Source code
.checkClusterLegendList Source code
.checkClusterMatrix Source code
.checkClusterTypes Source code
.checkClustersWithClusterLegend Source code
.checkCoClustering Source code
.checkDendroClusterFormat Source code
.checkDendroSamplesFormat Source code
.checkDendrogram Source code
.checkDissFunction Source code
.checkFunctionList Source code
.checkHasArgs Source code
.checkInput Source code
.checkMatch Source code
.checkMerge Source code
.checkOrderSamples Source code
.checkPrimaryIndex Source code
.checkTransform Source code
.claraCluster Source code
.clusterListToVector Source code
.clusterTrackingPlot Source code
.clusterVectorToList Source code
.clusterWrapper Source code
.clustersHammingDistance Source code
.colorby Source code
.convertOutListToCE Source code
.convertToAheatmap Source code
.convertToClusterLegend Source code
.convertToDendrogram Source code
.convertToNum Source code
.convertToPhyClasses Source code
.createDistNames Source code
.depricateArgument Source code
.diss01 Source code
.dissK Source code
.dupRemove Source code
.epsest.func Source code
.eraseMerge Source code
.force.ultrametric Source code
.genericClassify Source code
.getBestFGenes Source code
.getCheckValues Source code
.getClusterIds Source code
.getPassedArgs Source code
.hasOutBranch Source code
.hier01Cluster Source code
.hierKCluster Source code
.kmeansClassify Source code
.kmeansCluster Source code
.kmeansPartitionObject Source code
.m1_JC Source code
.m1_MB Source code
.m1_PC Source code
.m1_Storey Source code
.m1_adjP Source code
.m1_locfdr Source code
.makeArgsFromParam Source code
.makeClusterDendro Source code
.makeClusterFilterStats Source code
.makeClusterReducedRedo Source code
.makeColors Source code
.makeDiss Source code
.makeFakeBinary Source code
.makeIntegerClusters Source code
.makeIntegerMatrix Source code
.makeMergeDendrogram Source code
.makeNumeric Source code
.makePhylobaseTree Source code
.makeSampleDendro Source code
.makeSampleNames Source code
.makeTransFun Source code
.makeUnion Source code
.matchColors Source code
.matchToDendroData Source code
.mbkmeansClassify Source code
.mbkmeansCluster Source code
.mergePhylo Source code
.methodFormals Source code
.myTryFunc Source code
.mynote Source code
.nodeMergeInfo Source code
.orderByAlpha Source code
.pamClassify Source code
.pamCluster Source code
.pca Source code
.pcaDimRed Source code
.plotClustersInternal Source code
.plotDendro Source code
.postClusterMany Source code
.postProcessClusterK Source code
.pruneToNodes Source code
.pullColData Source code
.rcolors Source code
.removeOutbranch Source code
.safePhyloSubset Source code
.setClusterColors Source code
.setNodeLabels Source code
.speccCluster Source code
.testContrasts Source code
.testPhyloObject Source code
.testPrint Source code
.tightCluster Source code
.typeOfCoClustering Source code
.uniqueCluster Source code
.unnameClusterSlots Source code
.updateCurrentWorkflow Source code
.wrongArgsWarning Source code
ClusterExperiment Man page
ClusterExperiment,SingleCellExperiment,character-method Man page
ClusterExperiment,SingleCellExperiment,factor-method Man page
ClusterExperiment,SingleCellExperiment,matrix-method Man page
ClusterExperiment,SingleCellExperiment,numeric-method Man page
ClusterExperiment,SummarizedExperiment,ANY-method Man page
ClusterExperiment,matrixOrHDF5,ANY-method Man page
ClusterExperiment-class Man page
ClusterExperiment-methods Man page
ClusterFunction Man page
ClusterFunction,function-method Man page
ClusterFunction-class Man page
ClusterFunction-methods Man page
RSEC Man page
RSEC,ClusterExperiment-method Man page
RSEC,SingleCellExperiment-method Man page
RSEC,SummarizedExperiment-method Man page
RSEC,data.frame-method Man page
RSEC,matrix-method Man page
RSEC,matrixOrHDF5-method Man page
RSEC-methods Man page
[,ClusterExperiment,ANY,ANY,ANY-method Man page
[,ClusterExperiment,ANY,character,ANY-method Man page
[,ClusterExperiment,ANY,logical,ANY-method Man page
[,ClusterExperiment,ANY,numeric,ANY-method Man page
addClusterings Man page
addClusterings,ClusterExperiment,ClusterExperiment-method Man page
addClusterings,ClusterExperiment,matrix-method Man page
addClusterings,ClusterExperiment,vector-method Man page
addToColData Man page
addToColData,ClusterExperiment-method Man page
algorithmType Man page
algorithmType,ClusterFunction-method Man page
algorithmType,character-method Man page
algorithmType,factor-method Man page
algorithmType,list-method Man page
assignUnassigned Man page
assignUnassigned,ClusterExperiment-method Man page
bigPalette Man page
bubblePlot,table,table-method Man page
checkDendrogram Man page
checkDendrogram,ClusterExperiment,phylo4d,phylo4d-method Man page
checkRsecFluidigmObject Source code
clusterContrasts Man page
clusterContrasts,ClusterExperiment-method Man page
clusterContrasts,vector-method Man page
clusterDendrogram Man page
clusterDendrogram,ClusterExperiment-method Man page
clusterExperiment-deprecated Man page
clusterLabels Man page
clusterLabels,ClusterExperiment-method Man page
clusterLabels<- Man page
clusterLabels<-,ClusterExperiment,character-method Man page
clusterLegend Man page
clusterLegend,ClusterExperiment-method Man page
clusterLegend<- Man page
clusterLegend<-,ClusterExperiment,list-method Man page
clusterMany Man page
clusterMany,ClusterExperiment-method Man page
clusterMany,SingleCellExperiment-method Man page
clusterMany,SummarizedExperiment-method Man page
clusterMany,data.frame-method Man page
clusterMany,matrixOrHDF5-method Man page
clusterMatrix Man page
clusterMatrix,ClusterExperiment-method Man page
clusterMatrixColors Man page
clusterMatrixColors,ClusterExperiment-method Man page
clusterMatrixNamed Man page
clusterMatrixNamed,ClusterExperiment-method Man page
clusterSingle Man page
clusterSingle,ClusterExperiment-method Man page
clusterSingle,SingleCellExperiment-method Man page
clusterSingle,SummarizedExperiment-method Man page
clusterSingle,matrixOrHDF5OrNULL-method Man page
clusterTypes Man page
clusterTypes,ClusterExperiment-method Man page
clusterTypes<- Man page
clusterTypes<-,ClusterExperiment,character-method Man page
clusteringInfo Man page
clusteringInfo,ClusterExperiment-method Man page
coClustering Man page
coClustering,ClusterExperiment-method Man page
coClustering<- Man page
coClustering<-,ClusterExperiment,dsCMatrix-method Man page
coClustering<-,ClusterExperiment,matrix-method Man page
coClustering<-,ClusterExperiment,numeric-method Man page
colDataClusters Man page
colDataClusters,ClusterExperiment-method Man page
combineMany Man page
combineMany,ANY-method Man page
convertClusterLegend Man page
convertClusterLegend,ClusterExperiment-method Man page
convertToDendrogram Man page
convertToDendrogram,ClusterExperiment-method Man page
defaultNDims Man page
defaultNDims,SingleCellExperiment-method Man page
defaultNDims,matrixOrHDF5-method Man page
dendroClusterIndex Man page
dendroClusterIndex,ClusterExperiment-method Man page
eraseMergeInfo Man page
eraseMergeInfo,ClusterExperiment-method Man page
filterData Man page
filterData,SummarizedExperiment-method Man page
filterNames Man page
filterNames,SummarizedExperiment-method Man page
fluidigmColData Man page
fluidigmData Man page
getBestFeatures Man page
getBestFeatures,ClusterExperiment-method Man page
getBestFeatures,matrixOrHDF5-method Man page
getBuiltInFunction Man page
getBuiltInFunction,character-method Man page
getClusterIndex Man page
getClusterIndex,ClusterExperiment-method Man page
getClusterManyParams Man page
getClusterManyParams,ClusterExperiment-method Man page
getMergeCorrespond Man page
getMergeCorrespond,ClusterExperiment-method Man page
getPostProcessingArgs Man page
getPostProcessingArgs,ClusterFunction-method Man page
getReducedData Man page
getReducedData,ClusterExperiment-method Man page
getSingleClusterIndex Man page
getSingleClusterIndex,ClusterExperiment-method Man page
inputType Man page
inputType,ClusterFunction-method Man page
inputType,character-method Man page
inputType,factor-method Man page
inputType,list-method Man page
internalFunctionCheck Man page Source code
is.whole Source code
listBuiltInFilterStats Man page Source code
listBuiltInFunctions Man page Source code
listBuiltInReducedDims Man page Source code
listBuiltInType01 Man page Source code
listBuiltInTypeK Man page Source code
mainClustering Man page
mainClustering,ClusterFunction-method Man page
mainClustering,character-method Man page
makeBlankData Man page Source code
makeConsensus Man page
makeConsensus,ClusterExperiment-method Man page
makeConsensus,matrix-method Man page
makeDendrogram Man page
makeDendrogram,ClusterExperiment-method Man page
makeDendrogram,dist-method Man page
makeDendrogram,matrixOrHDF5-method Man page
makeFilterStats Man page
makeFilterStats,ClusterExperiment-method Man page
makeFilterStats,SummarizedExperiment-method Man page
makeFilterStats,matrixOrHDF5-method Man page
makeHashKey Source code
makeReducedDims Man page
makeReducedDims,ClusterExperiment-method Man page
makeReducedDims,SingleCellExperiment-method Man page
makeReducedDims,SummarizedExperiment-method Man page
makeReducedDims,matrixOrHDF5-method Man page
makeRsecFluidigmObject Man page Source code
massivePalette Man page
mergeClusterIndex Man page
mergeClusterIndex,ClusterExperiment-method Man page
mergeClusters Man page
mergeClusters,ClusterExperiment-method Man page
mergeClusters,matrixOrHDF5-method Man page
mergeCutoff Man page
mergeCutoff,ClusterExperiment-method Man page
mergeMethod Man page
mergeMethod,ClusterExperiment-method Man page
nClusterings Man page
nClusterings,ClusterExperiment-method Man page
nClusters Man page
nClusters,ClusterExperiment-method Man page
nFeatures Man page
nFeatures,ClusterExperiment-method Man page
nInternalNodes Man page
nInternalNodes,ClusterExperiment-method Man page
nNodes Man page
nNodes,ClusterExperiment-method Man page
nSamples Man page
nSamples,ClusterExperiment-method Man page
nTips Man page
nTips,ClusterExperiment-method Man page
nodeIds Man page
nodeIds,ClusterExperiment-method Man page
nodeLabels Man page
nodeLabels,ClusterExperiment-method Man page
nodeLabels<- Man page
nodeLabels<-,ClusterExperiment-method Man page
nodeMergeInfo Man page
nodeMergeInfo,ClusterExperiment-method Man page
numericalAsCharacter Man page Source code
orderSamples Man page
orderSamples,ClusterExperiment-method Man page
orderSamples<- Man page
orderSamples<-,ClusterExperiment,numeric-method Man page
otherIds Source code
plotBarplot Man page
plotBarplot,ClusterExperiment-method Man page
plotBarplot,matrix-method Man page
plotBarplot,vector-method Man page
plotClusterLegend Man page
plotClusterLegend,ClusterExperiment-method Man page
plotClusters Man page
plotClusters,ClusterExperiment-method Man page
plotClusters,matrix-method Man page
plotClustersTable Man page
plotClustersTable,ClusterExperiment-method Man page
plotClustersTable,table-method Man page
plotClustersWorkflow Man page
plotClustersWorkflow,ClusterExperiment-method Man page
plotCoClustering Man page
plotCoClustering,ClusterExperiment-method Man page
plotContrastHeatmap Man page
plotContrastHeatmap,ClusterExperiment-method Man page
plotDendrogram Man page
plotDendrogram,ClusterExperiment-method Man page
plotFeatureBoxplot Man page
plotFeatureBoxplot,ClusterExperiment,character-method Man page
plotFeatureBoxplot,ClusterExperiment,numeric-method Man page
plotFeatureScatter Man page
plotFeatureScatter,ClusterExperiment,character-method Man page
plotFeatureScatter,ClusterExperiment,numeric-method Man page
plotHeatmap Man page
plotHeatmap,ClusterExperiment-method Man page
plotHeatmap,ExpressionSet-method Man page
plotHeatmap,SingleCellExperiment-method Man page
plotHeatmap,SummarizedExperiment-method Man page
plotHeatmap,data.frame-method Man page
plotHeatmap,matrixOrHDF5-method Man page
plotHeatmap,table-method Man page
plotReducedDims Man page
plotReducedDims,ClusterExperiment-method Man page
plottingFunctions Man page
primaryCluster Man page
primaryCluster,ClusterExperiment-method Man page
primaryClusterIndex Man page
primaryClusterIndex,ClusterExperiment-method Man page
primaryClusterIndex<- Man page
primaryClusterIndex<-,ClusterExperiment,numeric-method Man page
primaryClusterLabel Man page
primaryClusterLabel,ClusterExperiment-method Man page
primaryClusterNamed Man page
primaryClusterNamed,ClusterExperiment-method Man page
primaryClusterType Man page
primaryClusterType,ClusterExperiment-method Man page
recolorClusters Man page
recolorClusters,ClusterExperiment,character-method Man page
reduceFunctions Man page
removeClusterings Man page
removeClusterings,ClusterExperiment-method Man page
removeClusters Man page
removeClusters,ClusterExperiment-method Man page
removeUnassigned Man page
removeUnassigned,ClusterExperiment-method Man page
renameClusters Man page
renameClusters,ClusterExperiment,character-method Man page
requiredArgs Man page
requiredArgs,ClusterFunction-method Man page
requiredArgs,character-method Man page
requiredArgs,factor-method Man page
requiredArgs,list-method Man page
rsecFluidigm Man page
sampleDendrogram Man page
sampleDendrogram,ClusterExperiment-method Man page
searchForPairs Source code
search_pairs Man page Source code
seqCluster Man page Source code
seqPal1 Man page
seqPal2 Man page
seqPal3 Man page
seqPal4 Man page
seqPal5 Man page
setBreaks Man page Source code
setToCurrent Man page
setToCurrent,ClusterExperiment-method Man page
setToFinal Man page
setToFinal,ClusterExperiment-method Man page
show Man page
show,ClusterExperiment-method Man page
showHeatmapPalettes Man page Source code
showPalette Man page Source code
simCount Man page
simData Man page
splitHashKey Source code
subsampleClustering Man page
subsampleClustering,ClusterFunction-method Man page
subsampleClustering,character-method Man page
subsampleLoop Source code
subset Man page
subsetByCluster Man page
subsetByCluster,ClusterExperiment-method Man page
tableClusters Man page
tableClusters,ClusterExperiment-method Man page
transformData Man page
transformData,ClusterExperiment-method Man page
transformData,SingleCellExperiment-method Man page
transformData,SummarizedExperiment-method Man page
transformData,matrixOrHDF5-method Man page
transformation Man page
transformation,ClusterExperiment-method Man page
transformation<- Man page
transformation<-,ClusterExperiment,function-method Man page
trueCluster Man page
updateObject Man page
updateObject,ClusterExperiment-method Man page
workflowClusterDetails Man page
workflowClusterDetails,ClusterExperiment-method Man page
workflowClusterTable Man page
workflowClusterTable,ClusterExperiment-method Man page
workflowClusters Man page
workflowClusters,ClusterExperiment-method Man page
clusterExperiment documentation built on Feb. 11, 2021, 2 a.m.

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