Files in celda

CEllular Latent Dirichlet Allocation

README.md R/celda_G.R R/matrixSums.R R/celdatSNE.R R/semi_pheatmap.R R/celda_functions.R R/decon.R R/selectFeatures.R R/aaa.R R/plot_dr.R R/misc.R R/perplexity.R R/celdaGridSearch.R R/RcppExports.R R/findMarkersTree.R R/accessors.R R/celdaUMAP.R R/plot_decontx.R R/moduleHeatmap.R R/factorizeMatrix.R R/getDecisions.R R/geneSetEnrich.R R/initialize_clusters.R R/celda_C.R R/loglikelihood.R R/plotHeatmap.R R/celdatosce.R R/celda_heatmap.R R/split_clusters.R R/splitModule.R R/celda_CG.R R/elbow.R R/data.R R/clusterProbability.R R/simulateCells.R R/featureModuleLookup.R R/recursiveSplit.R R/diffExp.R R/celdaProbabilityMap.R R/topRank.R vignettes/decontX.Rmd vignettes/celda.Rmd man/plotDimReduceCluster.Rd man/plotMarkerDendro.Rd man/getDecisions.Rd man/simulateCells.Rd man/simulateContamination.Rd man/sampleLabel.Rd man/logLikelihoodHistory.Rd man/matrixNames.Rd man/celdaClusters.Rd man/celdaGSim.Rd man/fastNormPropLog.Rd man/retrieveFeatureIndex.Rd man/differentialExpression.Rd man/celdaCGMod.Rd man/bestLogLikelihood.Rd man/selectFeatures.Rd man/splitModule.Rd man/contaminationSim.Rd man/celdaPerplexity.Rd man/resamplePerplexity.Rd man/topRank.Rd man/params.Rd man/celdaHeatmap.Rd man/resList.Rd man/plotHeatmap.Rd man/celdaTsne.Rd man/plotDimReduceModule.Rd man/runParams.Rd man/celda_G.Rd man/celdaCGGridSearchRes.Rd man/celdaProbabilityMap.Rd man/featureModuleLookup.Rd man/plotDimReduceGrid.Rd man/sceCeldaCG.Rd man/recodeClusterZ.Rd man/sceCeldaG.Rd man/fastNormPropSqrt.Rd man/featureModuleTable.Rd man/celdaPerplexity-celdaList-method.Rd man/subsetCeldaList.Rd man/findMarkersTree.Rd man/countChecksum.Rd man/geneSetEnrich.Rd man/recursiveSplitCell.Rd man/plotMarkerHeatmap.Rd man/sampleCells.Rd man/celdaUmap.Rd man/availableModels.Rd man/normalizeCounts.Rd man/perplexity.Rd man/factorizeMatrix.Rd man/decontX.Rd man/plotGridSearchPerplexityDiff.Rd man/sceCeldaC.Rd man/logLikelihood.Rd man/plotGridSearchPerplexity.Rd man/appendCeldaList.Rd man/plotDimReduceFeature.Rd man/celdaCGSim.Rd man/clusterProbability.Rd man/moduleHeatmap.Rd man/eigenMatMultInt.Rd man/celdaGMod.Rd man/fastNormProp.Rd man/celdaModel.Rd man/sceCeldaCGGridSearch.Rd man/celda_C.Rd man/celdaCSim.Rd man/recursiveSplitModule.Rd man/celdaCMod.Rd man/celdatosce.Rd man/plotDecontXMarkerPercentage.Rd man/celdaModules.Rd man/compareCountMatrix.Rd man/selectBestModel.Rd man/countChecksum-celdaList-method.Rd man/celdaGridSearch.Rd man/plotDecontXContamination.Rd man/semiPheatmap.Rd man/celda.Rd man/distinctColors.Rd man/recodeClusterY.Rd man/plotCeldaViolin.Rd man/nonzero.Rd man/plotDecontXMarkerExpression.Rd man/celda_CG.Rd man/decontXcounts.Rd tests/testthat.R tests/testthat/test-matrixSums.R tests/testthat/test-decon.R tests/testthat/test-celda_G.R tests/testthat/test-celda_C.R tests/testthat/test-intialize_cluster.R tests/testthat/test-with_seed.R tests/testthat/test-celda-functions.R tests/testthat/test-celda_CG.R inst/doc/decontX.pdf inst/doc/celda.R inst/doc/decontX.Rmd inst/doc/decontX.R inst/doc/celda.Rmd inst/doc/celda.pdf