# Generated by roxygen2: do not edit by hand

 export(appendCeldaList)

 export(availableModels)

 export(bestLogLikelihood)

 export(celda)
 export(celdaGridSearch)
 export(celdaHeatmap)

 export(celdaPerplexity)

 export(celdaProbabilityMap)
 export(celdaTsne)

 export(celdaUmap)

 export(celda_C)
 export(celda_CG)
 export(celda_G)
 export(clusterProbability)

 export(clusters)

 export(compareCountMatrix)

 export(countChecksum)

 export(decontX)

 export(differentialExpression)

 export(distinctColors)

 export(factorizeMatrix)
 export(featureModuleLookup)

 export(featureModuleTable)

 export(geneSetEnrich)

 export(logLikelihood)

 export(logLikelihoodHistory)

 export(logLikelihoodcelda_C)
 export(logLikelihoodcelda_CG)
 export(logLikelihoodcelda_G)

 export(matrixNames)
 export(moduleHeatmap)
 export(normalizeCounts)

 export(params)

 export(perplexity)
 export(plotDimReduceCluster)
 export(plotDimReduceFeature)
 export(plotDimReduceGrid)
 export(plotDimReduceModule)
 export(plotGridSearchPerplexity)

 export(plotGridSearchPerplexitycelda_C)
 export(plotGridSearchPerplexitycelda_CG)
 export(plotGridSearchPerplexitycelda_G)

 export(plotHeatmap)
 export(recodeClusterY)
 export(recodeClusterZ)

 export(recursiveSplitCell)
 export(recursiveSplitModule)

 export(resList)
 export(resamplePerplexity)
 export(runParams)
 export(sampleLabel)
 export(selectBestModel)
 export(simulateCells)

 export(simulateCellscelda_C)
 export(simulateCellscelda_CG)
 export(simulateCellscelda_G)

 export(simulateContaminatedMatrix)

 export(subsetCeldaList)
 export(topRank)

 export(violinPlot)

 exportMethods(bestLogLikelihood)

 exportMethods(celdaHeatmap)

 exportMethods(celdaPerplexity)

 exportMethods(celdaProbabilityMap)
 exportMethods(celdaTsne)

 exportMethods(celdaUmap)

 exportMethods(clusterProbability)

 exportMethods(clusters)

 exportMethods(countChecksum)

 exportMethods(factorizeMatrix)
 exportMethods(featureModuleLookup)

 exportMethods(logLikelihoodHistory)
 exportMethods(matrixNames)
 exportMethods(params)

 exportMethods(perplexity)

 exportMethods(resList)
 exportMethods(runParams)
 exportMethods(sampleLabel)

 import(Rcpp)
 import(RcppEigen)

 import(SummarizedExperiment)
 import(data.table, except = c(melt, shift))

 import(foreach)

 import(ggplot2)

 import(grDevices)

 import(graphics)

 import(grid)

 import(gridExtra, except = c(combine))

 import(stats, except = c(start, end))

 importFrom(MAST,FromMatrix)
 importFrom(MAST,summary)
 importFrom(MAST,zlm)
 importFrom(MCMCprecision,fit_dirichlet)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(Rtsne,Rtsne)
 importFrom(S4Vectors,mcols)
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,assayNames)
 importFrom(SummarizedExperiment,colData)
 importFrom(data.table,as.data.table)
 importFrom(digest,digest)
 importFrom(doParallel,registerDoParallel)

 importFrom(enrichR,enrichr)

 importFrom(enrichR,listEnrichrDbs)
 importFrom(ggrepel,geom_text_repel)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,colors)
 importFrom(grDevices,hsv)
 importFrom(grDevices,rgb2hsv)

 importFrom(grid,grid.pretty)

 importFrom(grid,unit)
 importFrom(gridExtra,grid.arrange)
 importFrom(gtable,gtable)
 importFrom(gtable,gtable_add_grob)
 importFrom(gtable,gtable_height)
 importFrom(gtable,gtable_width)
 importFrom(matrixStats,logSumExp)
 importFrom(methods,.hasSlot)
 importFrom(methods,is)
 importFrom(methods,new)

 importFrom(plyr,.)

 importFrom(plyr,mapvalues)
 importFrom(reshape2,melt)

 importFrom(scales,brewer_pal)

 importFrom(scales,dscale)

 importFrom(scales,hue_pal)

 importFrom(stringi,stri_list2matrix)
 importFrom(umap,umap)
 importFrom(umap,umap.defaults)

 importFrom(withr,with_seed)

 useDynLib(celda,"_colSumByGroup")
 useDynLib(celda,"_colSumByGroupChange")
 useDynLib(celda,"_colSumByGroup_numeric")

 useDynLib(celda,"_perplexityG")

 useDynLib(celda,"_rowSumByGroup")
 useDynLib(celda,"_rowSumByGroupChange")
 useDynLib(celda,"_rowSumByGroup_numeric")