NAMESPACE

# Generated by roxygen2: do not edit by hand

export(analyze_tf_cobinding)
export(analyze_tf_overlap)
export(annotate_enhancers)
export(benchmark_enhancer_predictor)
export(build_database)
export(cache_data)
export(call_accessible_regions)
export(chromatin_state_categories)
export(classify_celltype_accessibility)
export(classify_chromatin_states)
export(epiRomicsS4)
export(epiRomics_annotate_putative)
export(epiRomics_build_dB)
export(epiRomics_cache_data)
export(epiRomics_cache_path)
export(epiRomics_chromatin_states)
export(epiRomics_chromatin_states_categories)
export(epiRomics_enhanceosome)
export(epiRomics_enhancer_predictor_to_ref)
export(epiRomics_enhancers_co_marks)
export(epiRomics_enhancers_filter)
export(epiRomics_filter_accessible)
export(epiRomics_has_cache)
export(epiRomics_putative_enhancers)
export(epiRomics_quick_view)
export(epiRomics_regions_of_interest)
export(epiRomics_tf_cobinding)
export(epiRomics_tf_overlap)
export(epiRomics_track_layer)
export(epiRomics_track_layer_fast)
export(epiRomics_track_layer_gene)
export(filter_accessible_regions)
export(filter_enhancers)
export(find_enhanceosomes)
export(find_enhancers_by_comarks)
export(find_putative_enhancers)
export(get_cache_path)
export(get_regions_of_interest)
export(has_cache)
export(make_example_bigwig)
export(make_example_database)
export(make_example_enhanceosome)
export(make_example_putative_enhancers)
export(maxCovBwCached)
export(maxCovFilesCached)
export(plot_gene_tracks)
export(plot_quick_view)
export(plot_signal_histogram)
export(plot_tracks)
export(plot_tracks_fast)
exportClasses(epiRomicsS4)
importFrom(AnnotationDbi,mapIds)
importFrom(AnnotationDbi,select)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,width)
importFrom(ChIPseeker,annotatePeak)
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,genes)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,countOverlaps)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,intersect)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,setdiff)
importFrom(GenomicRanges,trim)
importFrom(GenomicRanges,values)
importFrom(IRanges,IRanges)
importFrom(IRanges,subsetByOverlaps)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(annotatr,annotatr_cache)
importFrom(annotatr,build_annotations)
importFrom(annotatr,builtin_annotations)
importFrom(annotatr,read_annotations)
importFrom(data.table,"%like%")
importFrom(data.table,data.table)
importFrom(data.table,fcase)
importFrom(data.table,fread)
importFrom(digest,digest)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,postscript)
importFrom(grDevices,tiff)
importFrom(graphics,abline)
importFrom(graphics,arrows)
importFrom(graphics,axis)
importFrom(graphics,hist)
importFrom(graphics,layout)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rect)
importFrom(graphics,segments)
importFrom(graphics,text)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,setValidity)
importFrom(rtracklayer,BigWigFile)
importFrom(rtracklayer,BigWigSelection)
importFrom(rtracklayer,import)
importFrom(stats,as.dist)
importFrom(stats,density)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(tools,file_ext)
importFrom(utils,globalVariables)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,untar)