catGenes/NAMESPACE at main · domingoscardoso/catGenes · GitHub

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# Generated by roxygen2: do not edit by hand

export(abbrevGen)
export(alignSeqs)
export(catfullGenes)
export(catmultGenes)
export(combineFASTA)
export(convertAlign)
export(dropSeq)
export(evomodelCmds)
export(evomodelTest)
export(fastadframe)
export(mineMitochondrion)
export(minePlastome)
export(mineSeq)
export(mineTaxa)
export(mrbayesRun)
export(mrbayesStop)
export(nexusdframe)
export(phylipdframe)
export(plotPhylo)
export(run_catGenes)
export(splitTips)
export(writeNexus)
export(writePhylip)
import(R.utils)
import(ape)
import(cowplot)
import(dplyr)
import(flora)
import(ggplot2)
import(ggtext)
import(ggtree)
import(glue)
import(magrittr)
import(phangorn)
import(phytools)
import(rmarkdown)
import(shiny)
import(shinydashboard)
import(shinyjs)
import(stats)
import(stringr)
import(tibble)
import(tidyr)
importFrom(Biostrings,readDNAStringSet)
importFrom(R.utils,insert)
importFrom(ape,Ntip)
importFrom(ape,as.DNAbin)
importFrom(ape,base.freq)
importFrom(ape,read.FASTA)
importFrom(ape,read.GenBank)
importFrom(ape,read.nexus.data)
importFrom(ape,write.FASTA)
importFrom(ape,write.dna)
importFrom(cowplot,save_plot)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,filter)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(flora,remove.authors)
importFrom(geneviewer,gbk_features_to_df)
importFrom(geneviewer,read_gbk)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,annotation_custom)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,ggplotGrob)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,theme)
importFrom(ggtext,geom_richtext)
importFrom(ggtree,MRCA)
importFrom(ggtree,geom_hilight)
importFrom(ggtree,geom_point2)
importFrom(ggtree,geom_text2)
importFrom(ggtree,geom_tiplab)
importFrom(ggtree,geom_tree)
importFrom(ggtree,geom_treescale)
importFrom(ggtree,ggtree)
importFrom(ggtree,hexpand)
importFrom(ggtree,td_filter)
importFrom(ggtree,xlim_tree)
importFrom(glue,glue)
importFrom(magrittr,"%>%")
importFrom(msa,msa)
importFrom(msa,msaConvert)
importFrom(phangorn,Descendants)
importFrom(phangorn,modelTest)
importFrom(phangorn,pml.control)
importFrom(phangorn,read.phyDat)
importFrom(phytools,getDescendants)
importFrom(processx,process)
importFrom(rentrez,entrez_fetch)
importFrom(rentrez,entrez_search)
importFrom(rentrez,entrez_summary)
importFrom(stats,na.omit)
importFrom(stats,setNames)
importFrom(stringr,str_extract)
importFrom(stringr,str_extract_all)
importFrom(stringr,str_pad)
importFrom(stringr,str_trunc)
importFrom(tibble,add_column)
importFrom(tibble,tibble)
importFrom(tidyr,unite)
importFrom(tools,file_path_sans_ext)
importFrom(treeio,isTip)
importFrom(utils,head)
importFrom(utils,tail)
importFrom(utils,write.table)