# Generated by roxygen2: do not edit by hand

export(Enhancers)
export(alignment)
export(alignmentOne)
export(conservedMotifs)
export(getENCODEdata)
export(queryEncode)
export(saveAlignments)
export(searchTFBPS)
export(shuffle)
exportClasses(Enhancers)
exportMethods(`$<-`)
exportMethods(`$`)
exportMethods(`distance<-`)
exportMethods(`distance`)
exportMethods(`genome<-`)
exportMethods(`genome`)
exportMethods(`peaks<-`)
exportMethods(`peaks`)
exportMethods(`query_tfbp`)
exportMethods(`seqinfo`)
exportMethods(`tfbp`)
exportMethods(coerce)
exportMethods(getSeq)
exportMethods(show)
exportMethods(subset)
exportMethods(subsetByOverlaps)
import(GenomicRanges)
import(Rcpp)
import(methods)
importClassesFrom(BSgenome,BSgenome)
importClassesFrom(S4Vectors,Annotated)
importFrom(BiocFileCache,BiocFileCache)
importFrom(BiocFileCache,bfcrpath)
importFrom(BiocFileCache,getBFCOption)
importFrom(BiocGenerics,organism)
importFrom(BiocGenerics,score)
importFrom(BiocParallel,bplapply)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,DNAMultipleAlignment)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,RNAStringSet)
importFrom(Biostrings,alphabetFrequency)
importFrom(Biostrings,consensusMatrix)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,injectHardMask)
importFrom(Biostrings,mask)
importFrom(Biostrings,matchPattern)
importFrom(Biostrings,pairwiseAlignment)
importFrom(Biostrings,pattern)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,unaligned)
importFrom(Biostrings,unmasked)
importFrom(Biostrings,write.phylip)
importFrom(GenomeInfoDb,"genome<-")
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,mapGenomeBuilds)
importFrom(GenomeInfoDb,seqinfo)
importFrom(IRanges,IRanges)
importFrom(IRanges,IRangesList)
importFrom(IRanges,Views)
importFrom(IRanges,gaps)
importFrom(IRanges,subject)
importFrom(IRanges,subsetByOverlaps)
importFrom(Matrix,Matrix)
importFrom(S4Vectors,extractROWS)
importFrom(httr,GET)
importFrom(httr,add_headers)
importFrom(httr,content)
importFrom(httr,http_error)
importFrom(httr,http_status)
importFrom(httr,http_type)
importFrom(jsonlite,fromJSON)
importFrom(methods,is)
importFrom(motifmatchr,matchMotifs)
importFrom(motifmatchr,motifMatches)
importFrom(rtracklayer,import)
importFrom(stats,p.adjust)
importFrom(utils,combn)
importFrom(utils,head)
importFrom(utils,tail)
importFrom(utils,write.csv)
importMethodsFrom(Biostrings,getSeq)
importMethodsFrom(Biostrings,reverseComplement)
importMethodsFrom(GenomeInfoDb,"genome<-")
importMethodsFrom(GenomeInfoDb,genome)
importMethodsFrom(GenomeInfoDb,seqinfo)
importMethodsFrom(IRanges,subsetByOverlaps)
importMethodsFrom(Matrix,rowSums)
importMethodsFrom(Matrix,t)
useDynLib(enhancerHomologSearch)