# Generated by roxygen2: do not edit by hand

export(adjustSignaturesForRegionSet)
export(composeGenomesFromExposures)
export(computeExplainedVariance)
export(convertAlexandrov2Shiraishi)
export(convertGenomesFromVRanges)
export(decomposeTumorGenomes)
export(determineSignatureDistances)
export(downgradeShiraishiSignatures)
export(evaluateDecompositionQuality)
export(getGenomesFromMutFeatData)
export(getSignaturesFromEstParam)
export(isAlexandrovSet)
export(isExposureSet)
export(isShiraishiSet)
export(isSignatureSet)
export(mapSignatureSets)
export(plotDecomposedContribution)
export(plotExplainedVariance)
export(plotMutationDistribution)
export(readAlexandrovSignatures)
export(readGenomesFromMPF)
export(readGenomesFromVCF)
export(readShiraishiSignatures)
export(sameSignatureFormat)
import(ggplot2)
importFrom(BSgenome.Hsapiens.UCSC.hg19,BSgenome.Hsapiens.UCSC.hg19)
importFrom(BiocGenerics,strand)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,oligonucleotideFrequency)
importFrom(Biostrings,reverseComplement)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,ranges)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqinfo)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,trim)
importFrom(Matrix,nearPD)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(SummarizedExperiment,rowRanges)
importFrom(TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg19.knownGene)
importFrom(VariantAnnotation,alt)
importFrom(VariantAnnotation,asVCF)
importFrom(VariantAnnotation,expand)
importFrom(VariantAnnotation,geno)
importFrom(VariantAnnotation,header)
importFrom(VariantAnnotation,isSNV)
importFrom(VariantAnnotation,readVcf)
importFrom(VariantAnnotation,readVcfAsVRanges)
importFrom(VariantAnnotation,ref)
importFrom(data.table,as.data.table)
importFrom(ggplot2,aes)
importFrom(ggplot2,dup_axis)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,rel)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggseqlogo,ggseqlogo)
importFrom(ggseqlogo,make_col_scheme)
importFrom(graphics,abline)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(gridExtra,grid.arrange)
importFrom(methods,.hasSlot)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(plyr,aaply)
importFrom(plyr,alply)
importFrom(plyr,compact)
importFrom(readxl,excel_format)
importFrom(readxl,read_excel)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,scatter.smooth)
importFrom(utils,combn)
importFrom(utils,read.table)
