# Generated by roxygen2: do not edit by hand

export(DbscanCluster)
export(TsneCluster)
export(conclusCacheClear)
export(loadDataOrMatrix)
export(retrieveFromGEO)
export(runCONCLUS)
export(singlecellRNAseq)
exportClasses(scRNAseq)
exportMethods("setCellsSimilarityMatrix<-")
exportMethods("setClustering<-")
exportMethods("setClustersMarkers<-")
exportMethods("setClustersSimilarityMatrix<-")
exportMethods("setClustersSimiliratyOrdered<-")
exportMethods("setCoordinates<-")
exportMethods("setCountMatrix<-")
exportMethods("setDbscanList<-")
exportMethods("setEpsilon<-")
exportMethods("setExperimentName<-")
exportMethods("setGenesInfos<-")
exportMethods("setMarkerGenesList<-")
exportMethods("setMinPoints<-")
exportMethods("setName<-")
exportMethods("setOutputDirectory<-")
exportMethods("setPC<-")
exportMethods("setPerplexity<-")
exportMethods("setSceNorm<-")
exportMethods("setSpecies<-")
exportMethods("setTSNEList<-")
exportMethods(addClustering)
exportMethods(calculateClustersSimilarity)
exportMethods(clusterCellsInternal)
exportMethods(exportResults)
exportMethods(generateTSNECoordinates)
exportMethods(getCellsSimilarityMatrix)
exportMethods(getClustering)
exportMethods(getClustersMarkers)
exportMethods(getClustersSimilarityMatrix)
exportMethods(getClustersSimilarityOrdered)
exportMethods(getCoordinates)
exportMethods(getCountMatrix)
exportMethods(getDbscanList)
exportMethods(getEpsilon)
exportMethods(getExperimentName)
exportMethods(getGenesInfos)
exportMethods(getMarkerGenesList)
exportMethods(getMinPoints)
exportMethods(getName)
exportMethods(getOutputDirectory)
exportMethods(getPC)
exportMethods(getPerplexity)
exportMethods(getSceNorm)
exportMethods(getSpecies)
exportMethods(getTSNEList)
exportMethods(normaliseCountMatrix)
exportMethods(plotCellHeatmap)
exportMethods(plotCellSimilarity)
exportMethods(plotClusteredTSNE)
exportMethods(plotClustersSimilarity)
exportMethods(plotGeneExpression)
exportMethods(rankGenes)
exportMethods(retrieveGenesInfo)
exportMethods(retrieveTableClustersCells)
exportMethods(retrieveTopClustersMarkers)
exportMethods(runDBSCAN)
exportMethods(testClustering)
import(BiocFileCache)
import(Rtsne)
import(doParallel)
importFrom(AnnotationDbi,keys)
importFrom(AnnotationDbi,select)
importFrom(Biobase,exprs)
importFrom(GEOquery,getGEO)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,sizeFactors)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useEnsembl)
importFrom(biomaRt,useMart)
importFrom(clusterProfiler,bitr)
importFrom(dbscan,kNNdistplot)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,"%>%")
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,summarise)
importFrom(factoextra,fviz_cluster)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(fpc,dbscan)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_gradientn)
importFrom(ggplot2,theme_bw)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.new)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(graphics,abline)
importFrom(gridExtra,grid.arrange)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,validObject)
importFrom(parallel,makeCluster)
importFrom(parallel,stopCluster)
importFrom(pheatmap,pheatmap)
importFrom(scales,alpha)
importFrom(scater,logNormCounts)
importFrom(scran,computeSumFactors)
importFrom(scran,quickCluster)
importFrom(stats,as.dist)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,pt)
importFrom(stats,quantile)
importFrom(stats,var)
importFrom(stringr,str_extract)
importFrom(tools,R_user_dir)
importFrom(utils,capture.output)
importFrom(utils,download.file)
importFrom(utils,globalVariables)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,write.csv)
importFrom(utils,write.table)
