# Generated by roxygen2: do not edit by hand

export(addCDS)
export(addExons)
export(addIds)
export(getTximetaBFC)
export(loadLinkedTxome)
export(makeDGEList)
export(makeLinkedTxome)
export(retrieveCDNA)
export(retrieveDb)
export(setTximetaBFC)
export(splitSE)
export(tximeta)
exportMethods(summarizeToGene)
importFrom(AnnotationDbi,keys)
importFrom(AnnotationDbi,loadDb)
importFrom(AnnotationDbi,mapIds)
importFrom(AnnotationDbi,saveDb)
importFrom(AnnotationDbi,select)
importFrom(AnnotationHub,AnnotationHub)
importFrom(AnnotationHub,dbconn)
importFrom(AnnotationHub,dbfile)
importFrom(AnnotationHub,query)
importFrom(BiocFileCache,BiocFileCache)
importFrom(BiocFileCache,bfcadd)
importFrom(BiocFileCache,bfccount)
importFrom(BiocFileCache,bfcnew)
importFrom(BiocFileCache,bfcquery)
importFrom(BiocFileCache,bfcrpath)
importFrom(Biostrings,"%in%")
importFrom(Biostrings,readDNAStringSet)
importFrom(GenomeInfoDb,"genome<-")
importFrom(GenomeInfoDb,"seqinfo<-")
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomicFeatures,cdsBy)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,"end<-")
importFrom(GenomicRanges,"start<-")
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(IRanges,CharacterList)
importFrom(IRanges,LogicalList)
importFrom(IRanges,NumericList)
importFrom(Matrix,sparseMatrix)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(ensembldb,EnsDb)
importFrom(ensembldb,ensDbFromGtf)
importFrom(jsonlite,fromJSON)
importFrom(jsonlite,toJSON)
importFrom(methods,as)
importFrom(methods,is)
importFrom(tibble,tibble)
importFrom(tools,R_user_dir)
importFrom(tools,file_ext)
importFrom(txdbmaker,makeTxDbFromGFF)
importFrom(txdbmaker,makeTxDbFromGRanges)
importFrom(tximport,summarizeToGene)
importFrom(tximport,tximport)
importFrom(utils,head)
importFrom(utils,menu)
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
