# Generated by roxygen2: do not edit by hand

S3method("[",Coordinate)
S3method("[",NCBI_Genome)
S3method("[",UCSC_Genome)
export(Coordinate)
export(EXPLORE)
export(Kmer_Table)
export(SCORE)
export(STUDY_ACROSS_POPULATIONS)
export(STUDY_ACROSS_SPECIES)
export(STUDY_CANCER_GENES)
export(STUDY_GENIC_ELEMENTS)
export(addAlphaCol)
export(bedToCoor)
export(buildControl)
export(buildMidPatternKmerTable)
export(buildRESTurl)
export(buildRangedKmerTable)
export(calKmerSkew)
export(calPWM)
export(catHeader)
export(countBaseComposition)
export(countChoppedKmers)
export(countDistribution)
export(countKmers)
export(countMidPatternContext2)
export(countMidPatternKmers)
export(countPointContext2)
export(countRangedKmers)
export(countRevCompKmers)
export(countSlidingWindow)
export(countSlidingWindow2)
export(count_substring_fixed)
export(count_substring_regex)
export(downloadNCBIGenomes)
export(downloadUCSCgenome)
export(extractKmers)
export(generateGenicElementCoor)
export(generateIntergenicCoor)
export(getCOSMICauthURL)
export(getCOSMICcancerGeneCensus)
export(getCOSMIClatestVersion)
export(getCOSMICmutantExport)
export(getEnsemblData)
export(getEnsemblRegionFeatures)
export(getEnsemblVariantFeatures)
export(getEnsemblVariantFeatures_serial)
export(getGnomADvariants)
export(getICTVvirusMetadataResource)
export(getNCBIassemblySummary)
export(getScores)
export(getUCSCgenePredTable)
export(getVCFmetainfo)
export(initKmerTable)
export(kmeRtone)
export(loadCoordinate)
export(loadGenome)
export(loadGenomicContents)
export(mapKmers)
export(mergeCoordinate)
export(mixColors)
export(partitionCoordinate)
export(persistentDownload)
export(readBED)
export(readFASTA)
export(readVCF)
export(readVCF2)
export(removeRegion)
export(reverseComplement)
export(scoreKmers)
export(selectRepresentativeFromASM)
export(splitFASTA)
export(trimCoordinate)
export(writeBED)
export(writeFASTA)
export(writeVCF)
import(data.table)
import(stringi)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,oligonucleotideFrequency)
importFrom(Biostrings,reverseComplement)
importFrom(R6,R6Class)
importFrom(Rcpp,evalCpp)
importFrom(RcppSimdJson,fparse)
importFrom(curl,curl_fetch_disk)
importFrom(curl,curl_fetch_memory)
importFrom(curl,handle_setheaders)
importFrom(curl,handle_setopt)
importFrom(curl,multi_add)
importFrom(curl,multi_run)
importFrom(curl,new_handle)
importFrom(curl,new_pool)
importFrom(curl,parse_headers_list)
importFrom(data.table,.N)
importFrom(data.table,CJ)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,merge.data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,set)
importFrom(data.table,setDT)
importFrom(data.table,setalloccol)
importFrom(data.table,setcolorder)
importFrom(data.table,setkey)
importFrom(data.table,setkeyv)
importFrom(data.table,setnafill)
importFrom(data.table,setnames)
importFrom(data.table,setorder)
importFrom(data.table,setorderv)
importFrom(future,nbrOfWorkers)
importFrom(future.apply,future_lapply)
importFrom(grDevices,cairo_pdf)
importFrom(grDevices,col2rgb)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,arrows)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,box)
importFrom(graphics,boxplot)
importFrom(graphics,grconvertX)
importFrom(graphics,grconvertY)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,matlines)
importFrom(graphics,matplot)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rasterImage)
importFrom(graphics,rect)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(jsonlite,base64_enc)
importFrom(jsonlite,fromJSON)
importFrom(openxlsx,read.xlsx)
importFrom(progressr,progressor)
importFrom(seqLogo,makePWM)
importFrom(seqLogo,seqLogo)
importFrom(stats,C)
importFrom(stats,density)
importFrom(stats,end)
importFrom(stats,median)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,start)
importFrom(stats,wilcox.test)
importFrom(stringi,stri_count_fixed)
importFrom(stringi,stri_count_regex)
importFrom(stringi,stri_detect_fixed)
importFrom(stringi,stri_extract_all_regex)
importFrom(stringi,stri_extract_first_regex)
importFrom(stringi,stri_length)
importFrom(stringi,stri_locate_all_regex)
importFrom(stringi,stri_locate_first_regex)
importFrom(stringi,stri_match_all_regex)
importFrom(stringi,stri_paste)
importFrom(stringi,stri_replace_all_regex)
importFrom(stringi,stri_replace_first_fixed)
importFrom(stringi,stri_replace_first_regex)
importFrom(stringi,stri_replace_last_fixed)
importFrom(stringi,stri_reverse)
importFrom(stringi,stri_split_boundaries)
importFrom(stringi,stri_split_fixed)
importFrom(stringi,stri_split_regex)
importFrom(stringi,stri_startswith_fixed)
importFrom(stringi,stri_sub)
importFrom(stringi,stri_sub_replace)
importFrom(stringi,stri_sub_replace_all)
importFrom(stringi,stri_trans_char)
importFrom(stringi,stri_trans_tolower)
importFrom(stringi,stri_trans_toupper)
importFrom(utils,count.fields)
importFrom(utils,download.file)
importFrom(venneuler,venneuler)
useDynLib(kmeRtone, .registration = TRUE)
