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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(crosses_centromere)
export(export_process_plot)
export(get_centromere_regions)
export(get_reference_signatures)
export(get_subtelomere_coordinate)
export(get_subtelomere_regions)
export(import_ranges)
export(import_snvs)
export(import_vcf)
export(loh_test)
export(loh_test_bool)
export(lst_test)
export(lst_test_bool)
export(mutation_catalog)
export(nnls_exposures)
export(nnls_exposures_worker)
export(nnls_montecarlo)
export(plot_nnls_exposures)
export(run_snv)
export(run_test)
export(tai_test)
export(tai_test_bool)
export(test_multiple)
import(GenomeInfoDb)
import(GenomicRanges)
import(IRanges)
import(futile.logger)
import(ggplot2)
import(nnls)
import(parallel)
import(snowfall)
importFrom(BSgenome,getBSgenome)
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,ranges)
importFrom(GenomicRanges,seqnames)
importFrom(IRanges,CharacterList)
importFrom(IRanges,IRanges)
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(SomaticSignatures,motifMatrix)
importFrom(SomaticSignatures,mutationContext)
importFrom(SummarizedExperiment,rowRanges)
importFrom(VariantAnnotation,VRanges)
importFrom(VariantAnnotation,geno)
importFrom(VariantAnnotation,makeVRangesFromGRanges)
importFrom(VariantAnnotation,readVcf)
importFrom(plyr,ddply)
importFrom(snow,setDefaultClusterOptions)