# Generated by roxygen2: do not edit by hand

export(EC2gene)
export(annots_from_fa_GRanges)
export(annots_from_fa_df)
export(dl_transcriptome)
export(get_inflection)
export(get_knee_df)
export(get_velocity_files)
export(knee_plot)
export(make_sparse_matrix)
export(read_count_output)
export(read_velocity_output)
export(save_tr2g_bustools)
export(sort_tr2g)
export(species2dataset)
export(subset_annot)
export(tr2g_EnsDb)
export(tr2g_TxDb)
export(tr2g_ensembl)
export(tr2g_fasta)
export(tr2g_gff3)
export(tr2g_gtf)
export(transcript2gene)
exportMethods(get_velocity_files)
importClassesFrom(Matrix,dgCMatrix)
importFrom(AnnotationDbi,columns)
importFrom(AnnotationDbi,keys)
importFrom(AnnotationDbi,keytypes)
importFrom(AnnotationFilter,AnnotationFilterList)
importFrom(AnnotationFilter,SeqNameFilter)
importFrom(AnnotationFilter,TxIdFilter)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,"%in%")
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,writeXStringSet)
importFrom(GenomeInfoDb,"genome<-")
importFrom(GenomeInfoDb,"isCircular<-")
importFrom(GenomeInfoDb,"seqlevelsStyle<-")
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,genomeStyles)
importFrom(GenomeInfoDb,isCircular)
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,mapSeqlevels)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomicFeatures,"seqlevels<-")
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,extractTranscriptSeqs)
importFrom(GenomicRanges,"mcols<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,flank)
importFrom(GenomicRanges,intersect)
importFrom(GenomicRanges,punion)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,setdiff)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,union)
importFrom(IRanges,IRanges)
importFrom(Matrix,colSums)
importFrom(Matrix,readMM)
importFrom(Rcpp,sourceCpp)
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,revElements)
importFrom(S4Vectors,split)
importFrom(biomaRt,getBM)
importFrom(biomaRt,listEnsemblArchives)
importFrom(biomaRt,listMarts)
importFrom(biomaRt,searchDatasets)
importFrom(biomaRt,useMart)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,transmute)
importFrom(ensembldb,exonsBy)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotation_logticks)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_path)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_log10)
importFrom(magrittr,"%>%")
importFrom(methods,as)
importFrom(methods,is)
importFrom(plyranges,read_gff)
importFrom(plyranges,read_gff3)
importFrom(plyranges,write_gff)
importFrom(plyranges,write_gff3)
importFrom(stats,complete.cases)
importFrom(stats,setNames)
importFrom(stringr,str_detect)
importFrom(stringr,str_extract)
importFrom(stringr,str_remove)
importFrom(stringr,str_replace)
importFrom(stringr,str_split)
importFrom(tibble,tibble)
importFrom(tidyr,separate)
importFrom(tidyr,unite)
importFrom(utils,download.file)
importFrom(utils,read.table)
importFrom(utils,write.table)
importFrom(zeallot,"%<-%")
useDynLib(BUSpaRse)
