ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion


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Documentation for package ‘conclus’ version 1.2.0

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A C D E G L N P R S T

-- A --

addClustering addClustering
addClustering-method addClustering

-- C --

calculateClustersSimilarity calculateClustersSimilarity
calculateClustersSimilarity-method calculateClustersSimilarity
clusterCellsInternal clusterCellsInternal
clusterCellsInternal-method clusterCellsInternal
conclusCacheClear conclusCacheClear
constructors constructors

-- D --

Dbscan The Dbscan class
Dbscan-class The Dbscan class
DbscanCluster constructors

-- E --

exportResults exportResults
exportResults-method exportResults

-- G --

generateTSNECoordinates generateTSNECoordinates
generateTSNECoordinates-method generateTSNECoordinates
getCellsSimilarityMatrix getters
getCellsSimilarityMatrix-method getters
getClustering getters
getClustering-method getters
getClustersMarkers getters
getClustersMarkers-method getters
getClustersSimilarityMatrix getters
getClustersSimilarityMatrix-method getters
getClustersSimilarityOrdered getters
getClustersSimilarityOrdered-method getters
getCoordinates getters
getCoordinates-method getters
getCountMatrix getters
getCountMatrix-method getters
getDbscanList getters
getDbscanList-method getters
getEpsilon getters
getEpsilon-method getters
getExperimentName getters
getExperimentName-method getters
getGenesInfos getters
getGenesInfos-method getters
getMarkerGenesList getters
getMarkerGenesList-method getters
getMinPoints getters
getMinPoints-method getters
getName getters
getName-method getters
getOutputDirectory getters
getOutputDirectory-method getters
getPC getters
getPC-method getters
getPerplexity getters
getPerplexity-method getters
getSceNorm getters
getSceNorm-method getters
getSpecies getters
getSpecies-method getters
getSuggestedClustersNumber getters
getSuggestedClustersNumber-method getters
getters getters
getTSNEList getters
getTSNEList-method getters

-- L --

loadDataOrMatrix loadDataOrMatrix

-- N --

normaliseCountMatrix normaliseCountMatrix
normaliseCountMatrix-method normaliseCountMatrix

-- P --

plotCellHeatmap plotCellHeatmap
plotCellHeatmap-method plotCellHeatmap
plotCellSimilarity plotCellSimilarity
plotCellSimilarity-method plotCellSimilarity
plotClusteredTSNE plotClusteredTSNE
plotClusteredTSNE-method plotClusteredTSNE
plotClustersSimilarity plotClustersSimilarity
plotClustersSimilarity-method plotClustersSimilarity
plotGeneExpression plotGeneExpression
plotGeneExpression-method plotGeneExpression

-- R --

rankGenes rankGenes
rankGenes-method rankGenes
retrieveFromGEO retrieveFromGEO
retrieveGenesInfo retrieveGenesInfo
retrieveGenesInfo-method retrieveGenesInfo
retrieveTableClustersCells retrieveTableClustersCells
retrieveTableClustersCells-method retrieveTableClustersCells
retrieveTopClustersMarkers retrieveTopClustersMarkers
retrieveTopClustersMarkers-method retrieveTopClustersMarkers
runCONCLUS runCONCLUS
runDBSCAN runDBSCAN
runDBSCAN-method runDBSCAN

-- S --

scRNAseq The scRNAseq class
scRNAseq-class The scRNAseq class
setCellsSimilarityMatrix setters
setCellsSimilarityMatrix<- setters
setCellsSimilarityMatrix<--method setters
setClustering setters
setClustering<- setters
setClustering<--method setters
setClustersMarkers setters
setClustersMarkers<- setters
setClustersMarkers<--method setters
setClustersSimilarityMatrix setters
setClustersSimilarityMatrix<- setters
setClustersSimilarityMatrix<--method setters
setClustersSimiliratyOrdered setters
setClustersSimiliratyOrdered<- setters
setClustersSimiliratyOrdered<--method setters
setCoordinates setters
setCoordinates<- setters
setCoordinates<--method setters
setCountMatrix setters
setCountMatrix<- setters
setCountMatrix<--method setters
setDbscanList setters
setDbscanList<- setters
setDbscanList<--method setters
setEpsilon setters
setEpsilon<- setters
setEpsilon<--method setters
setExperimentName setters
setExperimentName<- setters
setExperimentName<--method setters
setGenesInfos setters
setGenesInfos<- setters
setGenesInfos<--method setters
setMarkerGenesList setters
setMarkerGenesList<- setters
setMarkerGenesList<--method setters
setMinPoints setters
setMinPoints<- setters
setMinPoints<--method setters
setName<- setters
setName<--method setters
setOutputDirectory setters
setOutputDirectory<- setters
setOutputDirectory<--method setters
setPC setters
setPC<- setters
setPC<--method setters
setPerplexity setters
setPerplexity<- setters
setPerplexity<--method setters
setSceNorm setters
setSceNorm<- setters
setSceNorm<--method setters
setSpecies setters
setSpecies<- setters
setSpecies<--method setters
setSuggestedClustersNumber setters
setSuggestedClustersNumber<- setters
setSuggestedClustersNumber<--method setters
setters setters
setTSNEList setters
setTSNEList<- setters
setTSNEList<--method setters
singlecellRNAseq constructors

-- T --

testClustering testClustering
testClustering-method testClustering
Tsne The Tsne class
Tsne-class The Tsne class
TsneCluster constructors