API for celda
CEllular Latent Dirichlet Allocation

Global functions
.Order Source code
.addAlternativeSplit Source code
.bgCalcLL Source code
.cCCalcEMProbZ Source code
.cCCalcGibbsProbZ Source code
.cCCalcLL Source code
.cCDecomposeCounts Source code
.cCGCalcLL Source code
.cCGDecomposeCounts Source code
.cCGSplitY Source code
.cCGSplitZ Source code
.cCReDecomposeCounts Source code
.cCSplitZ Source code
.cDCalcEMDecontamination Source code
.cDCalcEMbgDecontamination Source code
.cGCalcGibbsProbY Source code
.cGCalcLL Source code
.cGDecomposeCounts Source code
.cGReDecomposeCounts Source code
.cGSplitY Source code
.calculateDecontXBarplotPercent Source code
.calculateTsne Source code
.calculateUmap Source code
.celdaTsneC Source code
.celdaTsneCG Source code
.celdaTsneG Source code
.celdaUmapC Source code
.celdaUmapCG Source code
.celdaUmapG Source code
.celda_C Source code
.celda_CG Source code
.celda_G Source code
.checkCountsDecon Source code
.checkDelta Source code
.clusterMat Source code
.colSumByGroup Source code
.colSumByGroupChange Source code
.colSumByGroupNumeric Source code
.convertAnnotations Source code
.convertToDendrogram Source code
.cosine Source code
.cosineDist Source code
.createBranchPoints Source code
.createCountChecksum Source code
.curveElbow Source code
.deconCalcLL Source code
.decontX Source code
.decontXoneBatch Source code
.decontxInitializeZ Source code
.decontxInitializeZ_prevous Source code
.dist2d Source code
.drawAnnotationLegend Source code
.drawAnnotationNames Source code
.drawAnnotations Source code
.drawColnames Source code
.drawDendrogram Source code
.drawLegend Source code
.drawMain Source code
.drawMatrix Source code
.drawRownames Source code
.findCoordinates Source code
.findGaps Source code
.generateAnnotationColours Source code
.generateBreaks Source code
.generateTreeList Source code
.getGeneAUC Source code
.getPerformance Source code
.getSplit Source code
.heatmapMotor Source code
.hellingerDist Source code
.highlightClassLabel Source code
.identity2 Source code
.infoGainDensity Source code
.initializeCluster Source code
.initializeSplitY Source code
.initializeSplitZ Source code
.is.na2 Source code
.lo Source code
.logMessages Source code
.mapClass2features Source code
.normalizeLogProbs Source code
.perplexityGLogPx Source code
.predictClass Source code Source code
.prepareCountsForDimReductionCeldaC Source code
.prepareCountsForDimReductionCeldaCG Source code
.prepareCountsForDimReductionCeldaG Source code
.processCellLabels Source code
.processCounts Source code
.processPlotDecontXMarkerInupt Source code
.processSampleLabels Source code
.processdbscanEps Source code
.processvarGenes Source code
.psdet Source code
.rdirichlet Source code
.removeZeroVariance Source code
.reorderCeldaCG Source code
.reorderCeldaG Source code
.reorderCelda_C Source code
.resampleCountMatrix Source code
.resamplePerplexity Source code
.rowSumByGroup Source code
.rowSumByGroupChange Source code
.rowSumByGroupNumeric Source code
.sampleLl Source code
.scaleColours Source code
.scaleMat Source code
.scaleRows Source code
.scaleVecColours Source code
.secondDerivativeEstimate Source code
.simulateCellscelda_C Source code
.simulateCellscelda_CG Source code
.simulateCellscelda_G Source code
.simulateContaminatedMatrix Source code
.singleSplitY Source code
.singleSplitZ Source code
.spearmanDist Source code
.splitMetricIGpIGd Source code
.splitMetricModF1 Source code
.splitMetricPairwiseAUC Source code
.splitMetricRecursive Source code
.summarizeTree Source code
.validateCounts Source code
.wrapBranchHybrid Source code
.wrapSplitHybrid Source code
GET_FUN Source code
SET_FUN Source code
addLogLikelihood Source code
appendCeldaList Man page Source code
availableModels Man page
bestLogLikelihood Man page
bestLogLikelihood,celdaModel-method Man page
cG_CalcGibbsProbY Source code
cG_CalcGibbsProbY_fastRow Source code
cG_CalcGibbsProbY_ori Source code
cG_calcGibbsProbY_Simple Source code
calculateNativeMatrix Source code
celda Man page Source code
celdaCGGridSearchRes Man page
celdaCGMod Man page
celdaCGSim Man page
celdaCMod Man page
celdaCSim Man page
celdaGMod Man page
celdaGSim Man page
celdaGridSearch Man page Source code
celdaHeatmap Man page
celdaHeatmap,celda_C-method Man page
celdaHeatmap,celda_CG-method Man page
celdaHeatmap,celda_G-method Man page
celdaPerplexity Man page
celdaPerplexity,celdaList-method Man page
celdaProbabilityMap Man page
celdaProbabilityMap,celda_C-method Man page
celdaProbabilityMap,celda_CG-method Man page
celdaTsne Man page
celdaTsne,celda_C-method Man page
celdaTsne,celda_CG-method Man page
celdaTsne,celda_G-method Man page
celdaUmap Man page
celdaUmap,celda_C-method Man page
celdaUmap,celda_CG-method Man page
celdaUmap,celda_G-method Man page
celda_C Man page Source code
celda_CG Man page Source code
celda_G Man page Source code
clusterProbability Man page
clusterProbability,celda_C-method Man page
clusterProbability,celda_CG-method Man page
clusterProbability,celda_G-method Man page
clusters Man page
clusters,celdaModel-method Man page
compareCountMatrix Man page Source code
contaminationSim Man page
countChecksum Man page
countChecksum,celdaList-method Man page
decontX Man page
decontX,ANY-method Man page
decontX,SingleCellExperiment-method Man page
decontXEM Source code
decontXInitialize Source code
decontXLogLik Source code
decontXcounts Man page
decontXcounts<- Man page
differentialExpression Man page Source code
distinctColors Man page Source code
eigenMatMultInt Man page Source code
factorizeMatrix Man page
factorizeMatrix,celda_C-method Man page
factorizeMatrix,celda_CG-method Man page
factorizeMatrix,celda_G-method Man page
fastNormProp Man page Source code
fastNormPropLog Man page Source code
fastNormPropSqrt Man page Source code
featureModuleLookup Man page
featureModuleLookup,celda_C-method Man page
featureModuleLookup,celda_CG-method Man page
featureModuleLookup,celda_G-method Man page
featureModuleTable Man page Source code
findMarkersTree Man page Source code
geneSetEnrich Man page Source code
getDecisions Man page Source code Source code
logLikelihood Man page Source code
logLikelihoodHistory Man page
logLikelihoodHistory,celdaModel-method Man page
logLikelihoodcelda_C Man page Source code
logLikelihoodcelda_CG Man page Source code
logLikelihoodcelda_G Man page Source code
matrixNames Man page
matrixNames,celdaModel-method Man page
moduleHeatmap Man page Source code
ncharX Source code
nonzero Man page Source code
normalizeCounts Man page Source code
params Man page
params,celdaModel-method Man page
perplexity Man page
perplexity,celda_C-method Man page
perplexity,celda_CG-method Man page
perplexity,celda_G-method Man page
plotCeldaViolin Man page Source code
plotDecontXContamination Man page Source code
plotDecontXMarkerExpression Man page Source code
plotDecontXMarkerPercentage Man page Source code
plotDimReduceCluster Man page Source code
plotDimReduceFeature Man page Source code
plotDimReduceGrid Man page Source code
plotDimReduceModule Man page Source code
plotGridSearchPerplexity Man page Source code
plotGridSearchPerplexitycelda_C Man page Source code
plotGridSearchPerplexitycelda_CG Man page Source code
plotGridSearchPerplexitycelda_G Man page Source code
plotHeatmap Man page Source code
plotMarkerDendro Man page Source code
plotMarkerHeatmap Man page Source code
recodeClusterY Man page Source code
recodeClusterZ Man page Source code
recursiveSplitCell Man page Source code
recursiveSplitModule Man page Source code
resList Man page
resList,celdaList-method Man page
resamplePerplexity Man page Source code
retrieveFeatureIndex Man page Source code
runParams Man page
runParams,celdaList-method Man page
sampleCells Man page
sampleLabel Man page
sampleLabel,celdaModel-method Man page
selectBestModel Man page Source code
semiPheatmap Man page Source code
simulateCells Man page Source code
simulateCellscelda_C Man page Source code
simulateCellscelda_CG Man page Source code
simulateCellscelda_G Man page Source code
simulateContamination Man page Source code
subUnderscore Source code
subsetCeldaList Man page Source code
topRank Man page Source code
vplayout Source code
celda documentation built on June 9, 2020, 2 a.m.