# Generated by roxygen2: do not edit by hand

export(CompareWilcox)
export(CompareedgeRGLM)
export(annotToCol2)
export(annotation_from_merged_peaks)
export(calculate_CNA)
export(calculate_cyto_mat)
export(calculate_gain_or_loss)
export(calculate_logRatio_CNA)
export(choose_cluster_scExp)
export(colors_scExp)
export(comparable_variables)
export(consensus_clustering_scExp)
export(correlation_and_hierarchical_clust_scExp)
export(create_project_folder)
export(create_scDataset_raw)
export(create_scExp)
export(define_feature)
export(detect_samples)
export(differential_activation)
export(differential_analysis_scExp)
export(enrich_TF_ChEA3_genes)
export(enrich_TF_ChEA3_scExp)
export(exclude_features_scExp)
export(feature_annotation_scExp)
export(filter_correlated_cell_scExp)
export(filter_scExp)
export(find_clusters_louvain_scExp)
export(find_top_features)
export(gene_set_enrichment_analysis_scExp)
export(generate_analysis)
export(generate_coverage_tracks)
export(generate_report)
export(getExperimentNames)
export(getMainExperiment)
export(get_cyto_features)
export(get_genomic_coordinates)
export(get_most_variable_cyto)
export(get_pathway_mat_scExp)
export(has_genomic_coordinates)
export(import_scExp)
export(inter_correlation_scExp)
export(intra_correlation_scExp)
export(launchApp)
export(normalize_scExp)
export(num_cell_after_QC_filt_scExp)
export(num_cell_after_cor_filt_scExp)
export(num_cell_before_cor_filt_scExp)
export(num_cell_in_cluster_scExp)
export(num_cell_scExp)
export(plot_cluster_consensus_scExp)
export(plot_correlation_PCA_scExp)
export(plot_coverage_BigWig)
export(plot_differential_summary_scExp)
export(plot_differential_volcano_scExp)
export(plot_distribution_scExp)
export(plot_gain_or_loss_barplots)
export(plot_heatmap_scExp)
export(plot_inter_correlation_scExp)
export(plot_intra_correlation_scExp)
export(plot_most_contributing_features)
export(plot_percent_active_feature_scExp)
export(plot_pie_most_contributing_chr)
export(plot_reduced_dim_scExp)
export(plot_reduced_dim_scExp_CNA)
export(plot_top_TF_scExp)
export(plot_violin_feature_scExp)
export(preprocess_CPM)
export(preprocess_RPKM)
export(preprocess_TFIDF)
export(preprocess_TPM)
export(preprocess_feature_size_only)
export(preprocessing_filtering_and_reduction)
export(read_sparse_matrix)
export(rebin_matrix)
export(reduce_dims_scExp)
export(run_tsne_scExp)
export(subsample_scExp)
export(subset_bam_call_peaks)
export(summary_DA)
export(swapAltExp_sameColData)
export(table_enriched_genes_scExp)
export(wrapper_Signac_FeatureMatrix)
import(ggplot2)
import(shiny)
importFrom(BiocParallel,bplapply)
importFrom(ConsensusClusterPlus,ConsensusClusterPlus)
importFrom(ConsensusClusterPlus,calcICL)
importFrom(DT,datatable)
importFrom(DelayedArray,blockApply)
importFrom(DelayedArray,colAutoGrid)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,countOverlaps)
importFrom(GenomicRanges,distanceToNearest)
importFrom(GenomicRanges,duplicated)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,intersect)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,pintersect)
importFrom(GenomicRanges,ranges)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,score)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,sort.GenomicRanges)
importFrom(GenomicRanges,split)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,tileGenome)
importFrom(GenomicRanges,union)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(IRanges,findOverlapPairs)
importFrom(IRanges,subsetByOverlaps)
importFrom(Matrix,cbind2)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,readMM)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,t)
importFrom(Rcpp,evalCpp)
importFrom(Rsamtools,BamFileList)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,countBam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,mergeBam)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamWhat)
importFrom(Rtsne,Rtsne)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,altExpNames)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,mainExpName)
importFrom(SingleCellExperiment,normcounts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SingleCellExperiment,rowData)
importFrom(SingleCellExperiment,swapAltExp)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(SummarizedExperiment,seqnames)
importFrom(batchelor,fastMNN)
importFrom(colorRamps,matlab.like)
importFrom(colourpicker,colourInput)
importFrom(colourpicker,updateColourInput)
importFrom(coop,pcor)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_rows)
importFrom(dplyr,desc)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_split)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,select)
importFrom(dplyr,slice_min)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_all)
importFrom(dplyr,tibble)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(forcats,fct_inorder)
importFrom(forcats,fct_reorder)
importFrom(fs,path_home)
importFrom(gggenes,geom_gene_arrow)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_label)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,hcl)
importFrom(grDevices,pdf)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,image)
importFrom(graphics,legend)
importFrom(graphics,par)
importFrom(graphics,pie)
importFrom(graphics,plot)
importFrom(gridExtra,grid.arrange)
importFrom(irlba,irlba)
importFrom(jsonlite,toJSON)
importFrom(kableExtra,cell_spec)
importFrom(kableExtra,group_rows)
importFrom(kableExtra,kable)
importFrom(kableExtra,kable_styling)
importFrom(matrixTests,col_wilcoxon_twosample)
importFrom(methods,as)
importFrom(methods,is)
importFrom(msigdbr,msigdbr)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(plotly,ggplotly)
importFrom(plotly,plotlyOutput)
importFrom(plotly,renderPlotly)
importFrom(qs2,qs_read)
importFrom(qs2,qs_save)
importFrom(qualV,LCS)
importFrom(rlist,list.append)
importFrom(rtracklayer,export.bed)
importFrom(rtracklayer,export.bw)
importFrom(rtracklayer,import)
importFrom(rtracklayer,import.bed)
importFrom(scater,readSparseCounts)
importFrom(scran,buildSNNGraph)
importFrom(scran,combineMarkers)
importFrom(scran,pairwiseWilcox)
importFrom(shinyFiles,parseDirPath)
importFrom(shinyFiles,shinyDirButton)
importFrom(shinyFiles,shinyDirChoose)
importFrom(shinyWidgets,chooseSliderSkin)
importFrom(shinyWidgets,materialSwitch)
importFrom(shinyWidgets,updateMaterialSwitch)
importFrom(shinycssloaders,withSpinner)
importFrom(shinydashboard,box)
importFrom(shinydashboard,dashboardBody)
importFrom(shinydashboard,menuItem)
importFrom(shinydashboard,sidebarMenu)
importFrom(shinydashboard,sidebarUserPanel)
importFrom(shinydashboard,tabItem)
importFrom(shinydashboard,tabItems)
importFrom(shinydashboardPlus,controlbarItem)
importFrom(shinydashboardPlus,controlbarMenu)
importFrom(shinydashboardPlus,dashboardControlbar)
importFrom(shinydashboardPlus,dashboardHeader)
importFrom(shinydashboardPlus,dashboardPage)
importFrom(shinydashboardPlus,dashboardSidebar)
importFrom(shinydashboardPlus,dropdownBlock)
importFrom(shinyhelper,helper)
importFrom(shinyhelper,observe_helpers)
importFrom(shinyjs,extendShinyjs)
importFrom(shinyjs,html)
importFrom(shinyjs,useShinyjs)
importFrom(stats,as.dist)
importFrom(stats,chisq.test)
importFrom(stats,cor)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,phyper)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(stats,wilcox.test)
importFrom(stringdist,stringdistmatrix)
importFrom(stringr,str_split_fixed)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,gather)
importFrom(tidyr,separate_rows)
importFrom(tidyr,unite)
importFrom(umap,umap)
importFrom(umap,umap.defaults)
importFrom(utils,data)
importFrom(utils,read.table)
importFrom(viridis,scale_color_viridis)
useDynLib(ChromSCape)
