Files in kharchenkolab/cacoa
Case-Control Analysis Tools for Single-Cell RNA-Seq
.Rbuildignore
.circleci/config.yml
.gitignore
CHANGELOG.md
CONTRIBUTING.md
DESCRIPTION
NAMESPACE
R/RcppExports.R
R/access_wrappers.R
R/cacoa.R
R/cell_density.R
R/cluster_free.R
R/coda.R
R/coda_balances.R
R/coda_checks.R
R/coda_plots.R
R/coda_tree.R
R/de_function.R
R/expression_distance.R
R/ontology.R
R/plot.R
R/stability.R
R/utils.R
README.md
man/Cacoa.Rd
man/addZScores.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/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/estimateCellDensityGraph.Rd
man/estimateCellDensityKde.Rd
man/estimateDEPerCellTypeInner.Rd
man/estimateExpressionChange.Rd
man/estimateGeneProgramsFabia.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/getCdaLoadings.Rd
man/getDEEntrezIdsSplitted.Rd
man/getDensityContour.Rd
man/getGenePalette.Rd
man/getLoadings.Rd
man/getLogFreq.Rd
man/getNodeBalances.Rd
man/getRndBalances.Rd
man/getRndPartition.Rd
man/getRndSbp.Rd
man/identifyFamilies.Rd
man/plotCellTypeSizeDep.Rd
man/plotContrastTree.Rd
man/plotCountBoxplotsPerType.Rd
man/plotDensityKde.Rd
man/plotHeatmap.Rd
man/plotMeanMedValuesPerCellType.Rd
man/plotNCellRegression.Rd
man/plotOntologyFamily.Rd
man/produceResampling.Rd
man/rblapply.Rd
man/removeGroupEffect.Rd
man/saveDEasJSON.Rd
man/sbp2tree.Rd
man/summarizeDEResamplingResults.Rd
man/theme_legend_position.Rd
man/validateDEPerCellTypeParams.Rd
man/wrap_strings.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/cluster_free.cpp
src/projdiff.cpp
src/utils.cpp
tests/testthat.R
tests/testthat/test_functions.R
vignettes/walkthrough_short.Rmd
