Files in kharchenkolab/cacoa

Case-Control Analysis Tools for Single-Cell RNA-Seq

CHANGELOG.md CONTRIBUTING.md R/RcppExports.R R/access_wrappers.R R/cacoa.R R/cell_density.R R/cluster_free.R R/coda.R R/de_function.R R/expression_distance.R R/metadata.R R/ontology.R R/plot.R R/stability.R R/utils.R README.md data-raw/panel_preprocessed.R man/Cacoa.Rd man/addZScores.Rd man/appendStatisticsToDE.Rd man/brewerPalette.Rd man/checkData.Rd man/checkDataAndCells.Rd man/checkDataGroups.Rd man/checkDataSbp.Rd man/checkDataTree.Rd man/checkGroups.Rd man/checkSbp.Rd man/checkSbpWhole.Rd man/checkTree.Rd man/clusterGOsPerType.Rd man/clusterIndividualGOs.Rd man/clusterOntologyDF.Rd man/clusteredOntologyDotplot.Rd man/collapseFamilies.Rd man/constructBestPartitionTree.Rd man/constructTree.Rd man/createDendrogram.Rd man/diffCellDensity.Rd man/distTreeOrder.Rd man/distanceBetweenTerms.Rd man/enrichGOOpt.Rd man/enrichGSEGOOpt.Rd man/estimateCdaSpace.Rd man/estimateCellDensityGraph.Rd man/estimateCellDensityKde.Rd man/estimateClusterPerGO.Rd man/estimateDEForTypeDESeq.Rd man/estimateDEForTypeEdgeR.Rd man/estimateDEForTypeLimma.Rd man/estimateDEForTypePairwiseStat.Rd man/estimateDEPerCellTypeInner.Rd man/estimateEnrichedGO.Rd man/estimateEnrichedGSEGO.Rd man/estimateExpressionChange.Rd man/estimateGeneProgramsFabia.Rd man/estimateOntologyClusterName.Rd man/estimateOntologyClusterNames.Rd man/estimateOntologyFamilies.Rd man/estimateOntologyFromIds.Rd man/extractCellGraph.Rd man/extractCellGroups.Rd man/extractEmbedding.Rd man/extractGeneExpression.Rd man/extractJointCountMatrix.Rd man/extractOdGenes.Rd man/extractRawCountMatrices.Rd man/extractSamplePerCell.Rd man/filterDEMetadata.Rd man/filterOntologies.Rd man/filterOntologyDf.Rd man/getDEEntrezIdsSplitted.Rd man/getDensityContour.Rd man/getExpressionFractionPerGroup.Rd man/getGenePalette.Rd man/getLoadings.Rd man/getLogFreq.Rd man/getNodeBalances.Rd man/getOntologyFamilyChildren.Rd man/getOntologyListLevels.Rd man/getRndBalances.Rd man/getRndPartition.Rd man/getRndSbp.Rd man/groupOntologiesByCluster.Rd man/identifyFamilies.Rd man/mapGeneIds.Rd man/normalizePseudoBulkMatrix.Rd man/plotCellLoadings.Rd man/plotCellTypeSizeDep.Rd man/plotCodaSpaceInner.Rd man/plotContrastTree.Rd man/plotCountBoxplotsPerType.Rd man/plotDensityKde.Rd man/plotHeatmap.Rd man/plotMeanMedValuesPerCellType.Rd man/plotNCellRegression.Rd man/plotOntologyFamily.Rd man/prepareSamplesForDE.Rd man/produceResampling.Rd man/rblapply.Rd man/removeGroupEffect.Rd man/sbp2tree.Rd man/strpart.Rd man/subsetMatricesWithCommonGenes.Rd man/summarizeDEResamplingResults.Rd man/theme_legend_position.Rd man/validateDEPerCellTypeParams.Rd man/wrap_strings.Rd tests/testthat.R tests/testthat/test_functions.R vignettes/walkthrough_short.Rmd