API for kharchenkolab/cacoa
Case-Control Analysis Tools for Single-Cell RNA-Seq
| Global functions | |
|---|---|
| Cacoa | Man page |
| addZScores | Man page Source code |
| adjacencyMatrixFromPaiwiseDists | Source code |
| adjustZScoresWithPermutations | Source code |
| appendStatisticsToDE | Man page |
| brewerPalette | Man page Source code |
| checkData | Man page |
| checkDataAndCells | Man page |
| checkDataGroups | Man page |
| checkDataSbp | Man page |
| checkDataTree | Man page |
| checkGroups | Man page |
| checkSbp | Man page |
| checkSbpWhole | Man page |
| checkTree | Man page |
| clusterFreeZScoreMat | Source code |
| clusterGOsPerType | Man page |
| clusterIndividualGOs | Man page |
| clusterOntologyDF | Man page |
| clusteredOntologyDotplot | Man page |
| collapseFamilies | Man page |
| colwiseBinaryDistance | Source code |
| constructBestPartitionTree | Man page |
| constructTree | Man page |
| createDendrogram | Man page |
| diffCellDensity | Man page |
| distTreeOrder | Man page |
| distanceBetweenTerms | Man page |
| enrichGOOpt | Man page |
| enrichGSEGOOpt | Man page |
| estimateCdaSpace | Man page |
| estimateCellDensityGraph | Man page |
| estimateCellDensityKde | Man page Source code |
| estimateClusterFreeExpressionShiftsC | Source code |
| estimateClusterFreeExpressionShiftsInfo | Source code |
| estimateClusterPerGO | Man page |
| estimateCorrelationDistance | Source code |
| estimateDEForTypeDESeq | Man page |
| estimateDEForTypeEdgeR | Man page |
| estimateDEForTypeLimma | Man page |
| estimateDEForTypePairwiseStat | Man page |
| estimateDEPerCellTypeInner | Man page |
| estimateEnrichedGO | Man page |
| estimateEnrichedGSEGO | Man page |
| estimateExpressionChange | Man page Source code |
| estimateGeneClustersLeiden | Source code |
| estimateGeneClustersPam | Source code |
| estimateGeneProgramsFabia | Man page Source code |
| estimateGraphVarianceSignificance | Source code |
| estimateOntologyClusterName | Man page |
| estimateOntologyClusterNames | Man page |
| estimateOntologyFamilies | Man page |
| estimateOntologyFromIds | Man page |
| estimateStabilityPerCellType | Source code |
| extractCellGraph | Man page Source code |
| extractCellGraph.Conos | Man page Source code |
| extractCellGraph.Seurat | Man page Source code |
| extractCellGroups | Man page Source code |
| extractCellGroups.Conos | Man page Source code |
| extractCellGroups.Seurat | Man page Source code |
| extractEmbedding | Man page |
| extractEmbedding.Conos | Man page |
| extractEmbedding.Seurat | Man page |
| extractGeneExpression | Man page |
| extractGeneExpression.Conos | Man page |
| extractGeneExpression.Seurat | Man page |
| extractGeneExpression.dgCMatrix | Man page |
| extractJointCountMatrix | Man page |
| extractJointCountMatrix.Conos | Man page |
| extractJointCountMatrix.Seurat | Man page |
| extractJointCountMatrix.dgCMatrix | Man page |
| extractOdGenes | Man page |
| extractOdGenes.Conos | Man page |
| extractOdGenes.Seurat | Man page |
| extractRawCountMatrices | Man page Source code |
| extractRawCountMatrices.Conos | Man page Source code |
| extractRawCountMatrices.Seurat | Man page Source code |
| extractRawCountMatrices.dgCMatrix | Man page |
| extractSamplePerCell | Man page |
| extractSamplePerCell.Conos | Man page |
| extractSamplePerCell.Seurat | Man page |
| filterDEMetadata | Man page |
| filterOntologies | Man page |
| filterOntologyDf | Man page |
| geneProgramSimilarityScores | Source code |
| getDEEntrezIdsSplitted | Man page Source code |
| getDensityContour | Man page |
| getExpressionFractionPerGroup | Man page |
| getGenePalette | Man page Source code |
| getLoadings | Man page Source code |
| getLogFreq | Man page |
| getNodeBalances | Man page |
| getOntologyFamilyChildren | Man page |
| getOntologyListLevels | Man page |
| getRndBalances | Man page |
| getRndPartition | Man page |
| getRndSbp | Man page |
| groupOntologiesByCluster | Man page |
| identifyFamilies | Man page |
| jaccardPwPval | Source code |
| jaccardPwTop | Source code |
| mapGeneIds | Man page Source code |
| mapIds | Source code |
| normalizePseudoBulkMatrix | Man page |
| plotCellLoadings | Man page |
| plotCellTypeSizeDep | Man page |
| plotCodaSpaceInner | Man page |
| plotContrastTree | Man page |
| plotCountBoxplotsPerType | Man page Source code |
| plotDensityKde | Man page |
| plotHeatmap | Man page Source code |
| plotMeanMedValuesPerCellType | Man page |
| plotNCellRegression | Man page Source code |
| plotOntologyFamily | Man page |
| plotStability | Source code |
| prepareOntologyPlotDF | Source code |
| prepareSamplesForDE | Man page Source code |
| produceResampling | Man page Source code |
| projdiff | Source code |
| rblapply | Man page Source code |
| removeGroupEffect | Man page |
| sbp2tree | Man page |
| strpart | Man page Source code |
| subsetMatricesWithCommonGenes | Man page Source code |
| summarizeDEResamplingResults | Man page |
| theme_legend_position | Man page Source code |
| validateDEPerCellTypeParams | Man page Source code |
| wrap_strings | Man page |
