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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(CRBHitsColors)
export(aa2rbh)
export(aadir2orthofinder)
export(aafile2rbh)
export(aafile2rbhplus)
export(cds2genepos)
export(cds2rbh)
export(cdsdir2orthofinder)
export(cdsfile2aafile)
export(cdsfile2rbh)
export(col2transparent)
export(filter_alnlen)
export(filter_eval)
export(filter_pident)
export(filter_qcov)
export(filter_rost1999)
export(filter_tcov)
export(gff2longest)
export(gtf2longest)
export(isoform2longest)
export(make_dagchainer)
export(make_last)
export(make_vignette)
export(plot_dagchainer)
export(plot_kaks)
export(rbh2dagchainer)
export(rbh2kaks)
export(seqid)
export(tandemdups)
importFrom(Biostrings,AAString)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,readAAStringSet)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,subseq)
importFrom(Biostrings,width)
importFrom(Biostrings,writeXStringSet)
importFrom(MSA2dist,cds2aa)
importFrom(MSA2dist,cds2codonaln)
importFrom(MSA2dist,dnastring2kaks)
importFrom(MSA2dist,indices2kaks)
importFrom(curl,curl_download)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_keys)
importFrom(dplyr,group_map)
importFrom(dplyr,group_split)
importFrom(dplyr,mutate)
importFrom(dplyr,reframe)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(foreach,"%do%")
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(ggplot2,aes)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_colour_continuous)
importFrom(ggplot2,scale_colour_manual)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,palette)
importFrom(grDevices,rgb)
importFrom(graphics,legend)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(gridExtra,grid.arrange)
importFrom(methods,is)
importFrom(methods,slot)
importFrom(parallel,makeForkCluster)
importFrom(parallel,stopCluster)
importFrom(readr,read_tsv)
importFrom(rlang,.data)
importFrom(stats,median)
importFrom(stats,setNames)
importFrom(stats,splinefun)
importFrom(stringr,str_split)
importFrom(stringr,str_split_fixed)
importFrom(stringr,str_sub)
importFrom(stringr,word)
importFrom(tidyr,"%>%")
importFrom(tidyr,unite)
importFrom(utils,combn)
importFrom(utils,read.table)
importFrom(utils,stack)
importFrom(utils,write.table)