campbio/celda
CEllular Latent Dirichlet Allocation

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392
Source code
47
Man pages
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campbio/celda: CEllular Latent Dirichlet Allocation
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API

API for campbio/celda
CEllular Latent Dirichlet Allocation

Global functions
.Order 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
.celdaCGWithSeed Source code
.celdaCWithSeed Source code
.celdaGWithSeed Source code
.celdaGridSearch Source code
.celdaHeatmapCelda_C Source code
.celdaHeatmapCelda_CG Source code
.celdaHeatmapCelda_G Source code
.celdaProbabilityMapC Source code
.celdaProbabilityMapCG Source code
.celdaTsne Source code
.celdaTsneC Source code
.celdaTsneCG Source code
.celdaTsneG Source code
.celdaUmap Source code
.celdaUmapC Source code
.celdaUmapCG Source code
.celdaUmapG Source code
.celda_C Source code
.celda_CG Source code
.celda_G Source code
.checkBackground Source code
.checkCountsDecon Source code
.checkDelta Source code
.clusterMat Source code
.clusterProbabilityCeldaC Source code
.clusterProbabilityCeldaCG Source code
.clusterProbabilityCeldaG Source code
.colSumByGroup Source code
.colSumByGroupChange Source code
.colSumByGroupChangeInteger Source code
.colSumByGroupChangeNumeric Source code
.colSumByGroupInteger Source code
.colSumByGroupNumeric Source code
.convertAnnotations Source code
.cosine Source code
.cosineDist Source code
.countsTimesProbs Source code
.createCountChecksum Source code
.createSCERecursiveSplitCell Source code
.createSCERecursiveSplitModule Source code
.createSCEceldaC Source code
.createSCEceldaCG Source code
.createSCEceldaG Source code
.createSCEceldaGridSearch Source code
.createSCEsimulateCellsCeldaC Source code
.createSCEsimulateCellsCeldaCG Source code
.createSCEsimulateCellsCeldaG 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
.factorizeMatrixC Source code
.factorizeMatrixCG Source code
.factorizeMatrixG Source code
.findCoordinates Source code
.findGaps Source code
.generateAnnotationColours Source code
.generateBreaks Source code
.heatmapMotor Source code
.hellingerDist Source code
.identity2 Source code
.initializeCluster Source code
.initializeSplitY Source code
.initializeSplitZ Source code
.is.na2 Source code
.lo Source code
.logLikelihoodcelda_C Source code
.logLikelihoodcelda_CG Source code
.logLikelihoodcelda_G Source code
.logMessages Source code
.normalizeLogProbs Source code
.perplexityCelda_C Source code
.perplexityCelda_CG Source code
.perplexityCelda_G Source code
.perplexityGLogPx Source code
.plotCeldaViolin Source code
.plotDimReduceCluster Source code
.plotDimReduceFeature Source code
.plotDimReduceGrid Source code
.plotDimReduceModule Source code
.plotGridSearchPerplexitycelda_C Source code
.plotGridSearchPerplexitycelda_CG Source code
.plotGridSearchPerplexitycelda_G Source code
.plotModuleHeatmap Source code
.plotRPCC Source code
.plotRPCCG Source code
.plotRPCG Source code
.prepareCountsForDimReductionCeldaC Source code
.prepareCountsForDimReductionCeldaCG Source code
.prepareCountsForDimReductionCeldaG Source code
.processCellLabels Source code
.processCounts Source code
.processPlotDecontXMarkerInupt Source code
.processReducedDim Source code
.processSampleLabels Source code
.processdbscanEps Source code
.processvarGenes Source code
.rdirichlet Source code
.recodeClusterY Source code
.recodeClusterZ Source code
.recursiveSplitCell Source code
.recursiveSplitCellWithSeed Source code
.recursiveSplitModule Source code
.recursiveSplitModuleWithSeed Source code
.reorderCeldaC Source code
.reorderCeldaCG Source code
.reorderCeldaCGsce Source code
.reorderCeldaCsce Source code
.reorderCeldaG Source code
.reorderCeldaGsce Source code
.resampleCountMatrix Source code
.resamplePerplexity Source code
.rowSumByGroup Source code
.rowSumByGroupChange Source code
.rowSumByGroupChangeInteger Source code
.rowSumByGroupChangeNumeric Source code
.rowSumByGroupInteger Source code
.rowSumByGroupNumeric Source code
.sampleLl Source code
.scaleColours Source code
.scaleMat Source code
.scaleRows Source code
.scaleVecColours Source code
.secondDerivativeEstimate Source code
.simulateCellsMaincelda_C Source code
.simulateCellsMaincelda_CG Source code
.simulateCellsMaincelda_G 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
.splitModule Source code
.splitModuleWithSeed Source code
.subsetCeldaListSCE Source code
.validateCounts 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,SingleCellExperiment-method 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
celdaClusters Man page
celdaClusters,SingleCellExperiment-method Man page
celdaClusters,celdaModel-method Man page
celdaClusters<- Man page
celdaClusters<-,SingleCellExperiment-method Man page
celdaGMod Man page
celdaGSim Man page
celdaGridSearch Man page
celdaGridSearch,SingleCellExperiment-method Man page
celdaGridSearch,matrix-method Man page
celdaHeatmap Man page
celdaHeatmap,SingleCellExperiment-method Man page
celdaModel Man page
celdaModel,SingleCellExperiment-method Man page
celdaModules Man page
celdaModules,SingleCellExperiment-method Man page
celdaModules<- Man page
celdaModules<-,SingleCellExperiment-method Man page
celdaPerplexity Man page
celdaPerplexity,celdaList-method Man page
celdaProbabilityMap Man page
celdaProbabilityMap,SingleCellExperiment-method Man page
celdaTsne Man page
celdaTsne,SingleCellExperiment-method Man page
celdaUmap Man page
celdaUmap,SingleCellExperiment-method Man page
celda_C Man page
celda_C,ANY-method Man page
celda_C,SingleCellExperiment-method Man page
celda_CG Man page
celda_CG,ANY-method Man page
celda_CG,SingleCellExperiment-method Man page
celda_G Man page
celda_G,ANY-method Man page
celda_G,SingleCellExperiment-method Man page
celdatosce Man page
celdatosce,celdaList-method Man page
celdatosce,celda_C-method Man page
celdatosce,celda_CG-method Man page
celdatosce,celda_G-method Man page
clusterProbability Man page
clusterProbability,SingleCellExperiment-method Man page
colSumByGroupChangeSparse Source code
colSumByGroupSparse Source code
compareCountMatrix Man page
compareCountMatrix,ANY,celdaList-method Man page
compareCountMatrix,ANY,celdaModel-method Man page
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,SingleCellExperiment-method Man page
decontXcounts<- Man page
decontXcounts<-,SingleCellExperiment-method Man page
distinctColors Man page Source code
eigenMatMultInt Man page Source code
eigenMatMultNumeric Man page Source code
factorizeMatrix Man page
factorizeMatrix,ANY,celda_C-method Man page
factorizeMatrix,ANY,celda_CG-method Man page
factorizeMatrix,ANY,celda_G-method Man page
factorizeMatrix,SingleCellExperiment,ANY-method Man page
fastNormProp Man page Source code
fastNormPropLog Man page Source code
fastNormPropSqrt Man page Source code
featureModuleLookup Man page
featureModuleLookup,SingleCellExperiment-method Man page
featureModuleTable Man page Source code
geneSetEnrich Man page
geneSetEnrich,SingleCellExperiment-method Man page
geneSetEnrich,matrix-method Man page
logLikelihood Man page
logLikelihood,SingleCellExperiment,ANY-method Man page
logLikelihood,matrix,celda_C-method Man page
logLikelihood,matrix,celda_CG-method Man page
logLikelihood,matrix,celda_G-method Man page
logLikelihoodHistory Man page
logLikelihoodHistory,SingleCellExperiment-method Man page
logLikelihoodHistory,celdaModel-method Man page
matrixNames Man page
matrixNames,celdaModel-method Man page
moduleHeatmap Man page
moduleHeatmap,SingleCellExperiment-method Man page
nonzero Man page Source code
normalizeCounts Man page Source code
params Man page
params,celdaModel-method Man page
perplexity Man page
perplexity,ANY,celda_C-method Man page
perplexity,ANY,celda_CG-method Man page
perplexity,ANY,celda_G-method Man page
perplexity,SingleCellExperiment,ANY-method Man page
plotCeldaViolin Man page
plotCeldaViolin,ANY-method Man page
plotCeldaViolin,SingleCellExperiment-method Man page
plotDecontXContamination Man page Source code
plotDecontXMarkerExpression Man page Source code
plotDecontXMarkerPercentage Man page Source code
plotDimReduceCluster Man page
plotDimReduceCluster,SingleCellExperiment-method Man page
plotDimReduceCluster,vector-method Man page
plotDimReduceFeature Man page
plotDimReduceFeature,ANY-method Man page
plotDimReduceFeature,SingleCellExperiment-method Man page
plotDimReduceGrid Man page
plotDimReduceGrid,ANY-method Man page
plotDimReduceGrid,SingleCellExperiment-method Man page
plotDimReduceModule Man page
plotDimReduceModule,ANY-method Man page
plotDimReduceModule,SingleCellExperiment-method Man page
plotGridSearchPerplexity Man page
plotGridSearchPerplexity,SingleCellExperiment-method Man page
plotGridSearchPerplexity,celdaList-method Man page
plotHeatmap Man page Source code
plotRPC Man page
plotRPC,SingleCellExperiment-method Man page
plotRPC,celdaList-method Man page
recodeClusterY Man page Source code
recodeClusterZ Man page Source code
recursiveSplitCell Man page
recursiveSplitCell,SingleCellExperiment-method Man page
recursiveSplitCell,matrix-method Man page
recursiveSplitModule Man page
recursiveSplitModule,SingleCellExperiment-method Man page
recursiveSplitModule,matrix-method Man page
reorderCelda Man page
reorderCelda,SingleCellExperiment,ANY-method Man page
reorderCelda,matrix,celda_C-method Man page
reorderCelda,matrix,celda_CG-method Man page
reorderCelda,matrix,celda_G-method Man page
reportCeldaCGPlotResults Man page Source code
reportCeldaCGRun Man page Source code
reportceldaCG Man page
resList Man page
resList,SingleCellExperiment-method Man page
resList,celdaList-method Man page
resamplePerplexity Man page
resamplePerplexity,ANY-method Man page
resamplePerplexity,SingleCellExperiment-method Man page
retrieveFeatureIndex Man page Source code
rowSumByGroupChangeSparse Source code
rowSumByGroupSparse Source code
runParams Man page
runParams,SingleCellExperiment-method Man page
runParams,celdaList-method Man page
sampleCells Man page
sampleLabel Man page
sampleLabel,SingleCellExperiment-method Man page
sampleLabel,celdaModel-method Man page
sampleLabel<- Man page
sampleLabel<-,SingleCellExperiment-method Man page
sceCeldaC Man page
sceCeldaCG Man page
sceCeldaCGGridSearch Man page
sceCeldaG Man page
selectBestModel Man page
selectBestModel,SingleCellExperiment-method Man page
selectBestModel,celdaList-method Man page
selectFeatures Man page
selectFeatures,SingleCellExperiment-method Man page
selectFeatures,matrix-method Man page
semiPheatmap Man page Source code
simulateCells Man page Source code
simulateContamination Man page Source code
splitModule Man page
splitModule,SingleCellExperiment-method Man page
subsetCeldaList Man page
subsetCeldaList,SingleCellExperiment-method Man page
subsetCeldaList,celdaList-method Man page
topRank Man page Source code
vplayout Source code
campbio/celda documentation built on April 5, 2024, 11:47 a.m.

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