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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(Converse_GeneIDSymbol)
export(Footprints_FOS)
export(Get_p2g_fun)
export(add_ENSID)
export(add_pseudotime)
export(add_regulation_type)
export(cal_footprint_cuts)
export(clustering_Kmeans)
export(combine_footprints)
export(diff_peaks)
export(enrich_module)
export(extract_expressed_TFs)
export(filter_ATAC)
export(filter_expression_profile)
export(filter_original_regulation)
export(filter_regulation_Rcis)
export(filter_regulation_fimo)
export(find_motifs)
export(find_motifs_targetgenes)
export(generate_fimo_regulation)
export(generate_peak_gtf)
export(generate_scATAC_Candid)
export(get_SmoothByBin_PseudotimeExp)
export(get_bed)
export(get_cor)
export(get_merged_fasta)
export(get_pseudotime)
export(get_related_genes)
export(get_related_peaks)
export(get_tss_region)
export(initiate_cy)
export(load_counts)
export(merge_sort_count)
export(network_analysis)
export(output_grn)
export(overlap_footprints_peaks)
export(plot_intramodular_network)
export(plot_kmeans_pheatmap)
export(plot_tf_network)
export(sort_TFs_degree)
import(ROCR)
import(dplyr)
import(ggplot2)
import(magrittr)
import(monocle)
import(pbapply)
import(sccore)
importFrom(BiocGenerics,estimateDispersions)
importFrom(BiocGenerics,estimateSizeFactors)
importFrom(Biostrings,readBStringSet)
importFrom(ChIPseeker,annotatePeak)
importFrom(DDRTree,DDRTree)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,countOverlaps)
importFrom(IRanges,IRanges)
importFrom(RCy3,createNetworkFromDataFrames)
importFrom(RCy3,createVisualStyle)
importFrom(RCy3,cytoscapePing)
importFrom(RCy3,cytoscapeVersionInfo)
importFrom(RCy3,layoutNetwork)
importFrom(RCy3,mapVisualProperty)
importFrom(RCy3,setVisualStyle)
importFrom(RcisTarget,cisTarget)
importFrom(RcisTarget,importRankings)
importFrom(Rsamtools,PileupParam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,pileup)
importFrom(VGAM,model.matrix)
importFrom(VGAM,negbinomial.size)
importFrom(clusterProfiler,bitr)
importFrom(clusterProfiler,enrichGO)
importFrom(clusterProfiler,enrichKEGG)
importFrom(dplyr,group_by)
importFrom(dplyr,summarise)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmFit)
importFrom(gridExtra,grid.arrange)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,layout_in_circle)
importFrom(igraph,layout_on_grid)
importFrom(igraph,layout_on_sphere)
importFrom(igraph,layout_randomly)
importFrom(monocle,newCellDataSet)
importFrom(monocle,orderCells)
importFrom(monocle,reduceDimension)
importFrom(parallel,makeCluster)
importFrom(parallel,stopCluster)
importFrom(pbmcapply,pbmcmapply)
importFrom(pheatmap,pheatmap)
importFrom(plyr,round_any)
importFrom(reshape2,melt)
importFrom(rlang,is_empty)
importFrom(sccore,plapply)
importFrom(stats,as.dist)
importFrom(stats,cor)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,p.adjust)
importFrom(stats,phyper)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(stringr,str_ends)
importFrom(utils,data)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,write.table)