# Generated by roxygen2: do not edit by hand

export(calcBaseline)
export(calcExpectedMutations)
export(calcObservedMutations)
export(calcTargetingDistance)
export(calculateMutability)
export(collapseClones)
export(createBaseline)
export(createMutabilityMatrix)
export(createMutationDefinition)
export(createRegionDefinition)
export(createSubstitutionMatrix)
export(createTargetingMatrix)
export(createTargetingModel)
export(distToNearest)
export(editBaseline)
export(expectedMutations)
export(extendMutabilityMatrix)
export(extendSubstitutionMatrix)
export(findThreshold)
export(groupBaseline)
export(makeAverage1merMut)
export(makeAverage1merSub)
export(makeDegenerate5merMut)
export(makeDegenerate5merSub)
export(minNumMutationsTune)
export(minNumSeqMutationsTune)
export(observedMutations)
export(plotBaselineDensity)
export(plotBaselineSummary)
export(plotDensityThreshold)
export(plotGmmThreshold)
export(plotMutability)
export(plotTune)
export(shmulateSeq)
export(shmulateTree)
export(slideWindowDb)
export(slideWindowSeq)
export(slideWindowTune)
export(slideWindowTunePlot)
export(summarizeBaseline)
export(testBaseline)
export(writeTargetingDistance)
exportClasses(Baseline)
exportClasses(DensityThreshold)
exportClasses(GmmThreshold)
exportClasses(MutationDefinition)
exportClasses(RegionDefinition)
exportClasses(TargetingModel)
exportMethods(plot)
exportMethods(print)
exportMethods(summary)
import(ggplot2)
import(graphics)
import(methods)
import(utils)
importFrom(KernSmooth,bkde)
importFrom(MASS,fitdistr)
importFrom(SDMTools,wt.sd)
importFrom(alakazam,IUPAC_DNA)
importFrom(alakazam,baseTheme)
importFrom(alakazam,checkColumns)
importFrom(alakazam,cpuCount)
importFrom(alakazam,getAAMatrix)
importFrom(alakazam,getAllele)
importFrom(alakazam,getDNAMatrix)
importFrom(alakazam,getFamily)
importFrom(alakazam,getGene)
importFrom(alakazam,getMRCA)
importFrom(alakazam,getPathLengths)
importFrom(alakazam,getSegment)
importFrom(alakazam,gridPlot)
importFrom(alakazam,groupGenes)
importFrom(alakazam,isValidAASeq)
importFrom(alakazam,nonsquareDist)
importFrom(alakazam,pairwiseDist)
importFrom(alakazam,pairwiseEqual)
importFrom(alakazam,progressBar)
importFrom(alakazam,seqDist)
importFrom(alakazam,seqEqual)
importFrom(alakazam,tableEdges)
importFrom(alakazam,translateStrings)
importFrom(ape,mst)
importFrom(diptest,dip.test)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,arrange_)
importFrom(dplyr,as_data_frame)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,combine)
importFrom(dplyr,data_frame)
importFrom(dplyr,data_frame_)
importFrom(dplyr,desc)
importFrom(dplyr,do)
importFrom(dplyr,filter)
importFrom(dplyr,filter_)
importFrom(dplyr,funs)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_)
importFrom(dplyr,mutate_at)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,rename_)
importFrom(dplyr,select)
importFrom(dplyr,select_)
importFrom(dplyr,summarize)
importFrom(dplyr,summarize_)
importFrom(dplyr,summarize_at)
importFrom(dplyr,transmute)
importFrom(dplyr,transmute_)
importFrom(dplyr,ungroup)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(foreach,registerDoSEQ)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,as_adjacency_matrix)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,set_vertex_attr)
importFrom(igraph,vertex_attr)
importFrom(iterators,icount)
importFrom(kedd,h.ucv)
importFrom(lazyeval,interp)
importFrom(progress,progress_bar)
importFrom(scales,log10_trans)
importFrom(scales,log2_trans)
importFrom(scales,math_format)
importFrom(scales,percent)
importFrom(scales,pretty_breaks)
importFrom(scales,scientific)
importFrom(scales,trans_breaks)
importFrom(scales,trans_format)
importFrom(seqinr,c2s)
importFrom(seqinr,s2c)
importFrom(seqinr,translate)
importFrom(seqinr,words)
importFrom(stats,approx)
importFrom(stats,convolve)
importFrom(stats,cor)
importFrom(stats,cov)
importFrom(stats,dbeta)
importFrom(stats,dgamma)
importFrom(stats,dnorm)
importFrom(stats,ecdf)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,na.exclude)
importFrom(stats,na.omit)
importFrom(stats,optim)
importFrom(stats,optimize)
importFrom(stats,p.adjust)
importFrom(stats,pbeta)
importFrom(stats,pgamma)
importFrom(stats,pnorm)
importFrom(stats,qbeta)
importFrom(stats,rbeta)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,uniroot)
importFrom(stats,weighted.mean)
importFrom(stringi,"stri_sub<-")
importFrom(stringi,stri_count_boundaries)
importFrom(stringi,stri_count_regex)
importFrom(stringi,stri_dup)
importFrom(stringi,stri_extract_all_regex)
importFrom(stringi,stri_extract_first_regex)
importFrom(stringi,stri_flatten)
importFrom(stringi,stri_join)
importFrom(stringi,stri_length)
importFrom(stringi,stri_replace_all_regex)
importFrom(stringi,stri_replace_first_regex)
importFrom(stringi,stri_sub)
importFrom(tidyr,gather)
importFrom(tidyr,gather_)
importFrom(tidyr,spread)
importFrom(tidyr,spread_)
