NAMESPACE

# Generated by roxygen2: do not edit by hand

export(annovarToMaf)
export(coOncoplot)
export(extractSignatures)
export(forestPlot)
export(geneCloud)
export(genesToBarcodes)
export(genotypeMatrix)
export(gisticBubblePlot)
export(gisticChromPlot)
export(gisticOncoPlot)
export(icgcSimpleMutationToMAF)
export(inferHeterogeneity)
export(lollipopPlot)
export(mafCompare)
export(mafSummary)
export(mafSurvival)
export(math.score)
export(mutCountMatrix)
export(oncodrive)
export(oncoplot)
export(oncostrip)
export(oncotate)
export(pancanComparison)
export(pfamDomains)
export(plotApobecDiff)
export(plotCBSsegments)
export(plotClusters)
export(plotOncodrive)
export(plotSignatures)
export(plotTiTv)
export(plotVaf)
export(plotmafSummary)
export(prepareMutSig)
export(rainfallPlot)
export(read.maf)
export(readGistic)
export(somaticInteractions)
export(subsetMaf)
export(tcgaCompare)
export(titv)
export(trinucleotideMatrix)
export(write.GisticSummary)
export(write.mafSummary)
exportClasses(GISTIC)
exportClasses(MAF)
exportMethods(getClinicalData)
exportMethods(getCytobandSummary)
exportMethods(getFields)
exportMethods(getGeneSummary)
exportMethods(getSampleSummary)
import(ComplexHeatmap)
import(RColorBrewer)
import(data.table)
import(ggplot2)
import(ggrepel)
import(grid)
import(methods)
import(survival)
importFrom(Biostrings,subseq)
importFrom(NMF,basis)
importFrom(NMF,coef)
importFrom(NMF,consensusmap)
importFrom(NMF,nmf)
importFrom(NMF,nmfEstimateRank)
importFrom(NMF,plot)
importFrom(Rsamtools,FaFile)
importFrom(VariantAnnotation,getSeq)
importFrom(VariantAnnotation,seqlevels)
importFrom(changepoint,cpt.mean)
importFrom(changepoint,cpts)
importFrom(cowplot,background_grid)
importFrom(cowplot,plot_grid)
importFrom(cowplot,save_plot)
importFrom(cowplot,theme_cowplot)
importFrom(grDevices,boxplot.stats)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(gridExtra,tableGrob)
importFrom(gridExtra,ttheme_minimal)
importFrom(mclust,densityMclust)
importFrom(rjson,fromJSON)
importFrom(wordcloud,wordcloud)