NAMESPACE

# Generated by roxygen2: do not edit by hand

export("%!in%")
export(NMF_Extraction)
export(RCircos.Get.Start.End.Locations_1)
export(RCircos.Heatmap.Plot_1)
export(RCircos.Link.Plot_1)
export(annotate_VCF)
export(bed2index)
export(chrTime_annot)
export(chrTime_plot)
export(cit.chromString2num)
export(cit.density)
export(cit.discretize)
export(cit.genomOrder)
export(cit.pangenomCoord)
export(cit.pangenomPlot)
export(cit.peaks)
export(cnaCCF_annot)
export(cnaCCF_plots)
export(compare_results)
export(count_triplets)
export(deconvolution_compare)
export(deconvolution_exposure)
export(deconvolution_fit)
export(deconvolution_fit_SV)
export(extract_dbs_from_vcf)
export(factoall)
export(factochar)
export(generate_table)
export(load2object)
export(makeMutypeMatFromVcf)
export(make_plot)
export(order_vcf)
export(palimpsest_CCFplot)
export(palimpsest_DissectSigs)
export(palimpsest_Fireworks)
export(palimpsest_addSVcategoriesToVcf)
export(palimpsest_clonalitySigsCompare)
export(palimpsest_cnvProfile)
export(palimpsest_dfPosXSegm)
export(palimpsest_distCosine)
export(palimpsest_input)
export(palimpsest_makeMutypeMatFromVcf)
export(palimpsest_plotTumorHistories)
export(plot.SV.sigs)
export(plot6mutationSpectrumFromVcf)
export(plot96mutationSpectrumFromVcf)
export(plotStrandBias6types)
export(plotStrandBias96types)
export(plotSubstypeNumberPerSample)
export(plot_signatures)
export(preprocessInput_sv)
export(rainfallz_plot)
export(signature_colour_generator)
export(signature_exposure_plot)
export(signature_origins)
import(Biostrings)
import(GenomicRanges)
import(NMF)
import(RCircos)
import(RColorBrewer)
import(VariantAnnotation)
import(ggplot2)
import(ggpubr)
import(gplots)
import(gtools)
import(lsa)
import(plotrix)
import(reshape2)
import(scales)
import(spgs)
import(tibble)
importFrom(Rgraphviz,pieGlyph)
importFrom(ggplot2,theme_bw)
importFrom(lsa,cosine)
importFrom(plotrix,draw.circle)
importFrom(reshape2,melt)