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

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Documentation for package ‘conclus’ version 1.2.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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
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
getTopMarkers	getters
getTopMarkers-method	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
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
setTopMarkers	setters
setTopMarkers<-	setters
setTopMarkers<--method	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