# Generated by roxygen2: do not edit by hand

export(LCD)
export(LCD_complex_cutoff)
export(LCD_complex_cutoff_combined)
export(LCD_complex_cutoff_consensus)
export(LCD_complex_cutoff_perPID)
export(LCD_extractCohort_callPerPID)
export(SMC)
export(SMC_perPID)
export(add_annotation)
export(add_as_fist_to_list)
export(aggregate_exposures_by_category)
export(annotate_intermut_dist_PID)
export(annotate_intermut_dist_cohort)
export(annotation_exposures_barplot)
export(annotation_exposures_list_barplot)
export(annotation_heatmap_exposures)
export(attribute_nucleotide_exchanges)
export(attribute_sequence_contex_indel)
export(attribution_of_indels)
export(average_over_present)
export(build_gene_list_for_pathway)
export(classify_indels)
export(compare_SMCs)
export(compare_exposures)
export(compare_expousre_sets)
export(compare_sets)
export(compare_to_catalogues)
export(complex_heatmap_exposures)
export(computeLogLik)
export(compute_comparison_stat_df)
export(confIntExp)
export(confidence_indel_calulation)
export(confidence_indel_only_calulation)
export(correct_rounded)
export(cosineDist)
export(cosineMatchDist)
export(create_indel_mut_cat_from_df)
export(create_indel_mutation_catalogue_from_df)
export(create_mutation_catalogue_from_VR)
export(create_mutation_catalogue_from_df)
export(cut_breaks_as_intervals)
export(deriveSigInd_df)
export(disambiguateVector)
export(enrichSigs)
export(exposures_barplot)
export(extract_names_from_gene_list)
export(find_affected_PIDs)
export(getSequenceContext)
export(get_extreme_PIDs)
export(hclust_exposures)
export(logLikelihood)
export(makeVRangesFromDataFrame)
export(make_catalogue_strata_df)
export(make_comparison_matrix)
export(make_strata_df)
export(make_subgroups_df)
export(melt_exposures)
export(merge_exposures)
export(normalizeMotifs_otherRownames)
export(normalize_df_per_dim)
export(plotExchangeSpectra)
export(plotExchangeSpectra_indel)
export(plotExposuresConfidence)
export(plotExposuresConfidence_indel)
export(plot_SMC)
export(plot_exposures)
export(plot_relative_exposures)
export(plot_strata)
export(read_entry)
export(read_list)
export(relateSigs)
export(repeat_df)
export(round_precision)
export(run_SMC)
export(run_annotate_vcf_pl)
export(run_comparison_catalogues)
export(run_comparison_general)
export(run_kmer_frequency_correction)
export(run_kmer_frequency_normalization)
export(run_plot_strata_general)
export(sd_over_present)
export(shapiro_if_possible)
export(split_exposures_by_subgroups)
export(stat_plot_subgroups)
export(stat_test_SMC)
export(stat_test_subgroups)
export(stderrmean)
export(stderrmean_over_present)
export(sum_over_list_of_df)
export(testSigs)
export(test_exposureAffected)
export(test_gene_list_in_exposures)
export(transform_rownames_MATLAB_to_R)
export(transform_rownames_R_to_MATLAB)
export(transform_rownames_YAPSA_to_deconstructSigs)
export(transform_rownames_deconstructSigs_to_YAPSA)
export(transform_rownames_nature_to_R)
export(translate_to_1kG)
export(translate_to_hg19)
export(trellis_rainfall_plot)
export(variateExp)
export(variateExpSingle)
import(BSgenome.Hsapiens.UCSC.hg19)
import(ComplexHeatmap)
import(GenomicRanges, except=c(subtract))
import(VariantAnnotation)
import(circlize)
import(dendextend)
import(dplyr, except = c(combine, select, setdiff, intersect,
  union))
import(ggplot2)
import(grid)
import(gridExtra)
import(gtrellis)
import(magrittr, except=c(subtract))
import(reshape2)
import(utils)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,matchPattern)
importFrom(Biostrings,subseq)
importFrom(Biostrings,xscat)
importFrom(GetoptLong,qq)
importFrom(GetoptLong,qq.options)
importFrom(KEGGREST,keggFind)
importFrom(KEGGREST,keggGet)
importFrom(KEGGREST,keggLink)
importFrom(PMCMRplus,kwAllPairsNemenyiTest)
importFrom(Seqinfo,"seqlengths<-")
importFrom(Seqinfo,"seqlevels<-")
importFrom(Seqinfo,seqlengths)
importFrom(Seqinfo,seqlevels)
importFrom(SomaticSignatures,motifMatrix)
importFrom(SomaticSignatures,mutationContext)
importFrom(SomaticSignatures,normalizeMotifs)
importFrom(circlize,rainfallTransform)
importFrom(corrplot,corrplot)
importFrom(doParallel,registerDoParallel)
importFrom(ggbeeswarm,geom_beeswarm)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rainbow)
importFrom(limSolve,lsei)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,mclapply)
importFrom(parallel,stopCluster)
importFrom(pracma,newtonsys)
importFrom(reshape2,melt)
