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

## Documentation for package ‘conclus’ version 1.0.0

- 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
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
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
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