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

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Functions
304
Source code
31
Man pages
27
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ilyessr/conclus: ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion
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API

API for ilyessr/conclus
ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

Global functions
.addCellsInfo Source code
.addGenesInfoCell Source code
.annotateEnsembl Source code
.annotateGenes Source code
.annotateRowData Source code
.annotateSymbols Source code
.buildMarkerGenesList Source code
.buildTTestFDR Source code
.buildTTestPval Source code
.buildingTsneObjects Source code
.callOrderCells Source code
.callOrderGenes Source code
.checkCache Source code
.checkClusteringMethod Source code
.checkCountMatrix Source code
.checkLoadedDataParams Source code
.checkObject Source code
.checkParamCellHeatmap Source code
.checkParamCellSimilarity Source code
.checkParamCellSimilaritySub Source code
.checkParamClustersSimilarity Source code
.checkParamDbScan Source code
.checkParamNorm Source code
.checkParamPlotGeneExpression Source code
.checkParamPlotTSNE Source code
.checkParamPlotTSNESub Source code
.checkParamSubFunction Source code
.checkParamTsne Source code
.checkParamsAddClustering Source code
.checkParamsClusterSim Source code
.checkParamsInternal Source code
.checkParamsRankGenes Source code
.checkParamsTests Source code
.checkParamsTopClust Source code
.checkParamsretrieveGenesInfo Source code
.checkRowAndColdata Source code
.choosePalette Source code
.computeClusMat Source code
.computePlotList Source code
.computeSimMat Source code
.conclusResult Source code
.convertToSymbols Source code
.createDbscanList Source code
.createFolder Source code
.createReportTable Source code
.createTSNEDir Source code
.dbscanComb Source code
.defineDatabase Source code
.defineMartVar Source code
.displayInfoMarkers Source code
.exportCSM Source code
.exportDBScan Source code
.exportGenesInfos Source code
.exportMarkers Source code
.exportNormInfo Source code
.exportTsne Source code
.fillGenesNumColumn Source code
.fillOneUmmiColumn Source code
.filterCells Source code
.filterGenes Source code
.filterSCE Source code
.filteringAndOrdering Source code
.generateAnnotationColors Source code
.getTSNEresults Source code
.groupGOandUniprotID Source code
.mergeColDataDf Source code
.mergeRowDataDf Source code
.mkDbscan Source code
.mkSimMat Source code
.mkSimMed Source code
.normalizeCon Source code
.orderCellsInCluster Source code
.orderClustersForHeatmap Source code
.orderCol Source code
.orderGenesInCluster Source code
.pheatmapClusterSim Source code
.pickDefaultPalette Source code
.plotAndSaveTSNE Source code
.plotCellH Source code
.plotCellSimilarityHeatmap Source code
.plotCellSimilarityOrderClusters Source code
.plotDistanceGraphWithEpsilon Source code
.plotTestClustering Source code
.printDBScan Source code
.printDist Source code
.printTSNE Source code
.queryBiomart Source code
.quickClusterScran Source code
.reinitializeObject Source code
.removeNoSymbol Source code
.retrieveClustersNumberK Source code
.retrieveColMetaDataFromSeries Source code
.retrieveColMetaDataFromURL Source code
.retrieveGenesInfoBiomart Source code
.retrieveMatrix Source code
.returnDB1 Source code
.returnDB2 Source code
.runAllSteps Source code
.runMarkersStep Source code
.runPlottingStep Source code
.runProcessingStep Source code
.saveAndPlotGeneExpression Source code
.saveCellSim Source code
.saveCellsSimilarityMatrix Source code
.saveClusteringResults Source code
.saveClustersSimilarityMatrix Source code
.saveDBScan Source code
.saveFullMarkers Source code
.saveGenesInfo Source code
.saveGenesInfos Source code
.saveHeatmap Source code
.saveNormalizedMatrix Source code
.savePlotClustersSim Source code
.saveTSNEPlot Source code
.saveTopMarkers Source code
.saveTsne Source code
.testCellsSimilarityMatrixSlot Source code
.testClustersSimilarityMatrixSlot Source code
.testClustersSimiliratyOrderedSlot Source code
.testCountMatrixSlot Source code
.testDbscanSlot Source code
.testExperimentNameSlot Source code
.testGenesInfosSlot Source code
.testGetMarkerGenesListSlot Source code
.testMattrixNames Source code
.testOutputDirectorySlot Source code
.testSpeciesSlot Source code
.testTopMarkersSlot Source code
.testsceNormSlot Source code
.testtSNEListSlot Source code
.tryGetBM Source code
.tryUseMart Source code
.writeDBScanResults Source code
.writeMarkersList Source code
.writeOutputTsne Source code
Dbscan Man page
Dbscan-class Man page
DbscanCluster Man page Source code
Tsne Man page
Tsne-class Man page
TsneCluster Man page Source code
addClustering Man page
addClustering,scRNAseq-method Man page
calculateClustersSimilarity Man page
calculateClustersSimilarity,scRNAseq-method Man page
checkGenesInfos Source code
checkList Source code
checkMarkerGenesList Source code
checkTopMarkers Source code
clusterCellsInternal Man page
clusterCellsInternal,scRNAseq-method Man page
conclusCacheClear Man page Source code
constructors Man page
createDirectory Source code
exportResults Man page
exportResults,scRNAseq-method Man page
generateTSNECoordinates Man page
generateTSNECoordinates,scRNAseq-method Man page
getCellsSimilarityMatrix Man page
getCellsSimilarityMatrix,scRNAseq-method Man page
getClustering Man page
getClustering,Dbscan-method Man page
getClustersSimilarityMatrix Man page
getClustersSimilarityMatrix,scRNAseq-method Man page
getClustersSimilarityOrdered Man page
getClustersSimilarityOrdered,scRNAseq-method Man page
getCoordinates Man page
getCoordinates,Tsne-method Man page
getCountMatrix Man page
getCountMatrix,scRNAseq-method Man page
getDbscanList Man page
getDbscanList,scRNAseq-method Man page
getEpsilon Man page
getEpsilon,Dbscan-method Man page
getExperimentName Man page
getExperimentName,scRNAseq-method Man page
getGenesInfos Man page
getGenesInfos,scRNAseq-method Man page
getMarkerGenesList Man page
getMarkerGenesList,scRNAseq-method Man page
getMinPoints Man page
getMinPoints,Dbscan-method Man page
getName Man page
getName,Dbscan-method Man page
getName,Tsne-method Man page
getOutputDirectory Man page
getOutputDirectory,scRNAseq-method Man page
getPC Man page
getPC,Tsne-method Man page
getPerplexity Man page
getPerplexity,Tsne-method Man page
getSceNorm Man page
getSceNorm,scRNAseq-method Man page
getSpecies Man page
getSpecies,scRNAseq-method Man page
getSuggestedClustersNumber Man page
getSuggestedClustersNumber,scRNAseq-method Man page
getTSNEList Man page
getTSNEList,scRNAseq-method Man page
getTopMarkers Man page
getTopMarkers,scRNAseq-method Man page
getters Man page
initialisePath Source code
loadDataOrMatrix Man page Source code
normaliseCountMatrix Man page
normaliseCountMatrix,scRNAseq-method Man page
plotCellHeatmap Man page
plotCellHeatmap,scRNAseq-method Man page
plotCellSimilarity Man page
plotCellSimilarity,scRNAseq-method Man page
plotClusteredTSNE Man page
plotClusteredTSNE,scRNAseq-method Man page
plotClustersSimilarity Man page
plotClustersSimilarity,scRNAseq-method Man page
plotGeneExpression Man page
plotGeneExpression,scRNAseq-method Man page
rankGenes Man page
rankGenes,scRNAseq-method Man page
retrieveFromGEO Man page Source code
retrieveGenesInfo Man page
retrieveGenesInfo,scRNAseq-method Man page
retrieveTableClustersCells Man page
retrieveTableClustersCells,scRNAseq-method Man page
retrieveTopClustersMarkers Man page
retrieveTopClustersMarkers,scRNAseq-method Man page
runCONCLUS Man page Source code
runDBSCAN Man page
runDBSCAN,scRNAseq-method Man page
scRNAseq Man page
scRNAseq-class Man page
setCellsSimilarityMatrix Man page
setCellsSimilarityMatrix<- Man page
setCellsSimilarityMatrix<-,scRNAseq-method Man page
setClustering Man page
setClustering<- Man page
setClustering<-,Dbscan-method Man page
setClustersSimilarityMatrix Man page
setClustersSimilarityMatrix<- Man page
setClustersSimilarityMatrix<-,scRNAseq-method Man page
setClustersSimiliratyOrdered Man page
setClustersSimiliratyOrdered<- Man page
setClustersSimiliratyOrdered<-,scRNAseq-method Man page
setCoordinates Man page
setCoordinates<- Man page
setCoordinates<-,Tsne-method Man page
setCountMatrix Man page
setCountMatrix<- Man page
setCountMatrix<-,scRNAseq-method Man page
setDbscanList Man page
setDbscanList<- Man page
setDbscanList<-,scRNAseq-method Man page
setEpsilon Man page
setEpsilon<- Man page
setEpsilon<-,Dbscan-method Man page
setExperimentName Man page
setExperimentName<- Man page
setExperimentName<-,scRNAseq-method Man page
setGenesInfos Man page
setGenesInfos<- Man page
setGenesInfos<-,scRNAseq-method Man page
setMarkerGenesList Man page
setMarkerGenesList<- Man page
setMarkerGenesList<-,scRNAseq-method Man page
setMinPoints Man page
setMinPoints<- Man page
setMinPoints<-,Dbscan-method Man page
setName<- Man page
setName<-,Dbscan-method Man page
setName<-,Tsne-method Man page
setOutputDirectory Man page
setOutputDirectory<- Man page
setOutputDirectory<-,scRNAseq-method Man page
setPC Man page
setPC<- Man page
setPC<-,Tsne-method Man page
setPerplexity Man page
setPerplexity<- Man page
setPerplexity<-,Tsne-method Man page
setSceNorm Man page
setSceNorm<- Man page
setSceNorm<-,scRNAseq-method Man page
setSpecies Man page
setSpecies<- Man page
setSpecies<-,scRNAseq-method Man page
setSuggestedClustersNumber Man page
setSuggestedClustersNumber<- Man page
setSuggestedClustersNumber<-,scRNAseq-method Man page
setTSNEList Man page
setTSNEList<- Man page
setTSNEList<-,scRNAseq-method Man page
setTopMarkers Man page
setTopMarkers<- Man page
setTopMarkers<-,scRNAseq-method Man page
setters Man page
singlecellRNAseq Man page Source code
testClustering Man page
testClustering,scRNAseq-method Man page
ilyessr/conclus documentation built on April 8, 2022, 1:43 p.m.

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