# Generated by roxygen2: do not edit by hand export(ERVmapParam) export(OneCodeToFindThemAll) export(TEtranscriptsParam) export(TelescopeParam) export(annotaTEs) export(atenaParam) export(getDNAtransposons) export(getLINEs) export(getLTRs) export(getSINEs) export(ovIntersectionStrict) export(ovUnion) export(rmskatenaparser) export(rmskbasicparser) export(rmskidentity) exportClasses(ERVmapParam) exportClasses(QuantifyParam) exportClasses(TEtranscriptsParam) exportClasses(TelescopeParam) exportClasses(atenaParam) exportMethods(features) exportMethods(path) exportMethods(qtex) exportMethods(show) importClassesFrom(GenomicAlignments,GAlignments) importClassesFrom(GenomicRanges,GenomicRanges_OR_GenomicRangesList) importClassesFrom(Matrix,lgCMatrix) importClassesFrom(Rsamtools,BamFileList) importFrom(AnnotationHub,AnnotationHub) importFrom(AnnotationHub,query) importFrom(BiocGenerics,basename) importFrom(BiocGenerics,path) importFrom(BiocParallel,SerialParam) importFrom(BiocParallel,bplapply) importFrom(GenomeInfoDb,"genome<-") importFrom(GenomeInfoDb,"seqinfo<-") importFrom(GenomeInfoDb,"seqlevels<-") importFrom(GenomeInfoDb,"seqlevelsStyle<-") importFrom(GenomeInfoDb,genome) importFrom(GenomeInfoDb,keepSeqlevels) importFrom(GenomeInfoDb,seqinfo) importFrom(GenomeInfoDb,seqlengths) importFrom(GenomeInfoDb,seqlevels) importFrom(GenomeInfoDb,seqlevelsStyle) importFrom(GenomeInfoDb,seqnames) importFrom(GenomicAlignments,cigar) importFrom(GenomicAlignments,explodeCigarOpLengths) importFrom(GenomicAlignments,extractAlignmentRangesOnReference) importFrom(GenomicAlignments,findOverlaps) importFrom(GenomicAlignments,first) importFrom(GenomicAlignments,qwidth) importFrom(GenomicAlignments,readGAlignmentPairs) importFrom(GenomicAlignments,readGAlignments) importFrom(GenomicAlignments,readGAlignmentsList) importFrom(GenomicAlignments,second) importFrom(GenomicAlignments,seqnames) importFrom(GenomicAlignments,start) importFrom(GenomicFeatures,features) importFrom(GenomicRanges,"mcols<-") importFrom(GenomicRanges,GRanges) importFrom(GenomicRanges,GRangesList) importFrom(GenomicRanges,end) importFrom(GenomicRanges,granges) importFrom(GenomicRanges,mcols) importFrom(GenomicRanges,pintersect) importFrom(GenomicRanges,reduce) importFrom(GenomicRanges,seqnames) importFrom(GenomicRanges,start) importFrom(GenomicRanges,strand) importFrom(GenomicRanges,width) importFrom(IRanges,CharacterList) importFrom(IRanges,IRanges) importFrom(IRanges,IRangesList) importFrom(IRanges,findOverlapPairs) importFrom(IRanges,mean) importFrom(IRanges,ranges) importFrom(IRanges,relist) importFrom(IRanges,unique) importFrom(Matrix,Matrix) importFrom(Matrix,colSums) importFrom(Matrix,rowSums) importFrom(Matrix,sparseMatrix) importFrom(Matrix,summary) importFrom(Matrix,t) importFrom(Matrix,which) importFrom(MatrixGenerics,rowRanges) importFrom(Rsamtools,"asMates<-") importFrom(Rsamtools,"yieldSize<-") importFrom(Rsamtools,BamFileList) importFrom(Rsamtools,ScanBamParam) importFrom(Rsamtools,asMates) importFrom(Rsamtools,bamFlagTest) importFrom(Rsamtools,scanBamFlag) importFrom(Rsamtools,scanBamHeader) importFrom(Rsamtools,yieldSize) importFrom(S4Vectors,DataFrame) importFrom(S4Vectors,Hits) importFrom(S4Vectors,List) importFrom(S4Vectors,Rle) importFrom(S4Vectors,countQueryHits) importFrom(S4Vectors,countSubjectHits) importFrom(S4Vectors,decode) importFrom(S4Vectors,first) importFrom(S4Vectors,from) importFrom(S4Vectors,isSorted) importFrom(S4Vectors,mcols) importFrom(S4Vectors,nLnode) importFrom(S4Vectors,nRnode) importFrom(S4Vectors,nrow) importFrom(S4Vectors,pc) importFrom(S4Vectors,queryHits) importFrom(S4Vectors,rownames) importFrom(S4Vectors,runValue) importFrom(S4Vectors,second) importFrom(S4Vectors,split) importFrom(S4Vectors,subjectHits) importFrom(S4Vectors,to) importFrom(SQUAREM,squarem) importFrom(SummarizedExperiment,SummarizedExperiment) importFrom(cli,cli_alert_info) importFrom(cli,cli_alert_success) importFrom(matrixStats,logSumExp) importFrom(methods,as) importFrom(methods,formalArgs) importFrom(methods,is) importFrom(methods,new) importFrom(methods,show) importFrom(sparseMatrixStats,colSums2) importFrom(sparseMatrixStats,rowMaxs) importFrom(sparseMatrixStats,rowSums2) importFrom(stats,aggregate) importFrom(stats,median) importFrom(stats,runif) importFrom(stats,setNames)