# 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")