NAMESPACE

# Generated by roxygen2: do not edit by hand

export(ClusteredSignal)
export(ClusteredSignal.fromConfig)
export(ClusteredSignal.null)
export(QcColorMapping)
export(QcConfig.files)
export(QcConfig.save_config)
export(QcConfigFeatures)
export(QcConfigFeatures.GRanges)
export(QcConfigFeatures.files)
export(QcConfigFeatures.null)
export(QcConfigFeatures.parse)
export(QcConfigFeatures.save_config)
export(QcConfigSignal)
export(QcConfigSignal.files)
export(QcConfigSignal.null)
export(QcConfigSignal.parse)
export(QcConfigSignal.save_config)
export(QcScaleColor)
export(QcScaleFill)
export(bfcif)
export(digest_args)
export(get_args)
export(get_feature_file_load_function)
export(get_mapped_reads)
export(guess_feature_file_format)
export(guess_read_mode)
export(make_anno_dt)
export(make_anno_grs)
export(make_assign_dt)
export(make_centered_query_gr)
export(make_dt)
export(make_feature_as_signal_dt)
export(make_feature_overlap_signal_profiles)
export(make_fq_dt)
export(make_frip_dt)
export(make_peak_dt)
export(make_scc_dt)
export(plot_anno_overlap)
export(plot_feature_comparison)
export(plot_feature_overlap_signal_profiles)
export(plot_fq_dt)
export(plot_scc_dt)
export(plot_signals)
export(sampleCap)
export(ssvQC)
export(ssvQC.plotCorrelation)
export(ssvQC.plotFRIP)
export(ssvQC.plotFeatures)
export(ssvQC.plotMappedReads)
export(ssvQC.plotSCC)
export(ssvQC.plotSignal)
export(ssvQC.prepCapValue)
export(ssvQC.prepCorrelation)
export(ssvQC.prepFRIP)
export(ssvQC.prepFeatures)
export(ssvQC.prepFetch)
export(ssvQC.prepFragLens)
export(ssvQC.prepMappedReads)
export(ssvQC.prepSCC)
export(ssvQC.prepSignal)
export(ssvQC.referenceUsesSameScale)
export(ssvQC.removeClusters)
export(ssvQC.removeFeatures)
export(ssvQC.runAll)
export(ssvQC.save_config)
export(ssvQC.selectClusters)
export(ssvQC.selectFeatures)
export(sync_height)
export(sync_width)
export(write_bed_frip)
export(write_bed_overlaps)
export(write_ssvQC.correlation)
export(write_ssvQC.per_peak)
export(write_ssvQC.summary)
exportClasses(ClusteredSignal)
exportClasses(QcConfig)
exportClasses(QcConfigFeatures)
exportClasses(QcConfigSignal)
exportClasses(QcPlot)
exportClasses(ssvQC.complete)
exportClasses(ssvQC.complete.bw)
exportClasses(ssvQC.featureOnly)
exportClasses(ssvQC.signalOnly)
exportClasses(ssvQC.signalOnly.bw)
exportMethods(QcColorMapping)
exportMethods(QcScaleColor)
exportMethods(QcScaleFill)
exportMethods(plot)
exportMethods(show)
import(BiocFileCache)
import(GenomeInfoDb)
import(GenomicRanges)
import(Rsamtools)
import(data.table, except = c(shift, first, second, last, melt, dcast))
import(digest)
import(ggplot2)
import(pbmcapply)
import(pheatmap)
import(rtracklayer)
import(seqsetvis)
import(tools)
importFrom(methods,new)
importFrom(pbapply,pblapply)
importFrom(pbmcapply,pbmclapply)
importFrom(reshape2,melt)
importFrom(scales,rescale)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(utils,read.table)