# Generated by roxygen2: do not edit by hand

export(aggregate_by_cell_bin)
export(aggregate_nearby_peaks)
export(annotate_cds_by_site)
export(assemble_connections)
export(build_gene_activity_matrix)
export(compare_connections)
export(df_for_coords)
export(estimate_distance_parameter)
export(find_overlapping_ccans)
export(find_overlapping_coordinates)
export(generate_ccans)
export(generate_cicero_models)
export(make_atac_cds)
export(make_cicero_cds)
export(normalize_gene_activities)
export(plot_accessibility_in_pseudotime)
export(plot_connections)
export(ranges_for_coords)
export(run_cicero)
import(Gviz)
import(VGAM)
import(data.table)
import(ggplot2)
import(monocle)
importFrom(Biobase,"fData<-")
importFrom(Biobase,"pData<-")
importFrom(Biobase,ExpressionSet)
importFrom(Biobase,annotatedDataFrameFrom)
importFrom(Biobase,assayDataNew)
importFrom(Biobase,exprs)
importFrom(Biobase,fData)
importFrom(Biobase,multiassign)
importFrom(Biobase,pData)
importFrom(BiocGenerics,estimateDispersions)
importFrom(BiocGenerics,estimateSizeFactors)
importFrom(IRanges,findOverlaps)
importFrom(data.table,melt.data.table)
importFrom(dplyr,"%>%")
importFrom(grDevices,col2rgb)
importFrom(grDevices,dev.cur)
importFrom(grDevices,dev.off)
importFrom(grDevices,palette)
importFrom(grDevices,rainbow)
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(plyr,.)
importFrom(stats,as.formula)
importFrom(stats,cov)
importFrom(stats,dist)
importFrom(stats,filter)
importFrom(stats,median)
importFrom(utils,combn)
importFrom(utils,read.table)
