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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(GCA2Lineage)
export(IPG2Lineage)
export(acc2FA)
export(acc2Lineage)
export(addLeaves2Alignment)
export(addLineage)
export(addName)
export(addTaxID)
export(alignFasta)
export(assignJobQueue)
export(calculateEstimatedWallTimeFromOpts)
export(calculateProcessRuntime)
export(cleanClusters)
export(cleanDomainArchitecture)
export(cleanGeneDescription)
export(cleanGenomicContext)
export(cleanLineage)
export(cleanSpecies)
export(combineFiles)
export(combineFullAnalysis)
export(combineIPR)
export(condenseRepeatedDomains)
export(convert2TitleCase)
export(convertAlignment2FA)
export(convertAlignment2Trees)
export(convertFA2Tree)
export(countByColumn)
export(createBinaryDomainNetwork)
export(createDomainNetwork)
export(createFA2Tree)
export(createGenomicContextNetwork)
export(createJobResultsURL)
export(createJobStatusEmailMessage)
export(createLineageLookup)
export(createMSA_Kalign)
export(createMSA_PDF)
export(createRepresentativeAccNum)
export(createUndirectedGenomicContextNetwork)
export(createWordCloud2Element)
export(createWordCloudElement)
export(downloadAssemblySummary)
export(efetchIPG)
export(extractAccNum)
export(filterByDomains)
export(filterByFrequency)
export(findParalogs)
export(formatJobArgumentsHTML)
export(generateAllAlignments2FA)
export(getAccNumFromFA)
export(getProcessRuntimeWeights)
export(getTopAccByLinDomArch)
export(mapAcc2Name)
export(mapAdvOption2Process)
export(mapOption2Process)
export(plotEstimatedWallTimes)
export(plotIPR2Viz)
export(plotIPR2VizWeb)
export(plotLineageDA)
export(plotLineageDomainRepeats)
export(plotLineageHeatmap)
export(plotLineageNeighbors)
export(plotLineageQuery)
export(plotLineageSunburst)
export(plotStackedLineage)
export(plotSunburst)
export(plotTreemap)
export(plotUpSet)
export(prepareColumnParams)
export(prepareSingleColumnParams)
export(proteinAcc2TaxID)
export(proteinAcc2TaxID_old)
export(removeAsterisks)
export(removeEmptyRows)
export(removeTails)
export(renameFA)
export(rename_fasta)
export(replaceQuestionMarks)
export(reverseOperonSeq)
export(runDeltaBlast)
export(runRPSBlast)
export(selectLongestDuplicate)
export(sendJobStatusEmail)
export(shortenLineage)
export(sinkReset)
export(straightenOperonSeq)
export(summarizeByLineage)
export(summarizeDomArch)
export(summarizeDomArch_ByLineage)
export(summarizeGenContext)
export(summarizeGenContext_ByDomArchLineage)
export(summarizeGenContext_ByLineage)
export(themeGenes2)
export(totalGenContextOrDomArchCounts)
export(validateCountDF)
export(wordcloud3)
export(writeMSA_AA2FA)
export(writeProcessRuntime2TSV)
export(writeProcessRuntime2YML)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,readAAStringSet)
importFrom(Biostrings,toString)
importFrom(Biostrings,unmasked)
importFrom(RColorBrewer,brewer.pal)
importFrom(UpSetR,upset)
importFrom(XVector,subseq)
importFrom(ape,write.tree)
importFrom(assertthat,assert_that)
importFrom(assertthat,has_name)
importFrom(base64enc,base64encode)
importFrom(biomartr,getKingdomAssemblySummary)
importFrom(d3r,d3_nest)
importFrom(data.table,as.data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,setnames)
importFrom(dplyr,across)
importFrom(dplyr,add_row)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_rows)
importFrom(dplyr,c_across)
importFrom(dplyr,count)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_at)
importFrom(dplyr,if_else)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,pull)
importFrom(dplyr,relocate)
importFrom(dplyr,right_join)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(dplyr,union)
importFrom(dplyr,where)
importFrom(fs,path_sanitize)
importFrom(furrr,future_map)
importFrom(future,future)
importFrom(future,plan)
importFrom(future,value)
importFrom(gggenes,geom_gene_arrow)
importFrom(gggenes,geom_subgene_arrow)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,as_labeller)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_grey)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,rainbow)
importFrom(here,here)
importFrom(htmltools,htmlTemplate)
importFrom(htmlwidgets,JS)
importFrom(htmlwidgets,createWidget)
importFrom(htmlwidgets,onRender)
importFrom(htmlwidgets,sizingPolicy)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,delete_vertices)
importFrom(igraph,graph_from_edgelist)
importFrom(igraph,layout.auto)
importFrom(igraph,layout.circle)
importFrom(igraph,layout_on_grid)
importFrom(igraph,layout_randomly)
importFrom(igraph,plot.igraph)
importFrom(igraph,vertex)
importFrom(magrittr,"%>%")
importFrom(msa,msa)
importFrom(msa,msaClustalOmega)
importFrom(msa,msaClustalW)
importFrom(msa,msaMuscle)
importFrom(msa,msaPrettyPrint)
importFrom(phangorn,NJ)
importFrom(phangorn,bootstrap.pml)
importFrom(phangorn,dist.ml)
importFrom(phangorn,modelTest)
importFrom(phangorn,optim.parsimony)
importFrom(phangorn,optim.pml)
importFrom(phangorn,phyDat)
importFrom(phangorn,plotBS)
importFrom(phangorn,pml)
importFrom(phangorn,pml.control)
importFrom(phangorn,pratchet)
importFrom(phangorn,read.phyDat)
importFrom(phangorn,upgma)
importFrom(plotly,plot_ly)
importFrom(purrr,as_vector)
importFrom(purrr,exec)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map_chr)
importFrom(purrr,pmap)
importFrom(purrr,pmap_dfr)
importFrom(readr,cols)
importFrom(readr,read_delim)
importFrom(readr,read_file)
importFrom(readr,read_lines)
importFrom(readr,read_tsv)
importFrom(readr,write_file)
importFrom(readr,write_lines)
importFrom(readr,write_tsv)
importFrom(rentrez,entrez_fetch)
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,abort)
importFrom(rlang,as_string)
importFrom(rlang,inform)
importFrom(rlang,sym)
importFrom(rlang,warn)
importFrom(sendmailR,mime_part)
importFrom(sendmailR,sendmail)
importFrom(seqinr,dist.alignment)
importFrom(seqinr,read.alignment)
importFrom(shiny,showNotification)
importFrom(stats,as.formula)
importFrom(stats,complete.cases)
importFrom(stats,logLik)
importFrom(stats,na.omit)
importFrom(stringi,stri_extract_all_regex)
importFrom(stringi,stri_replace_all_regex)
importFrom(stringr,coll)
importFrom(stringr,str_count)
importFrom(stringr,str_detect)
importFrom(stringr,str_glue)
importFrom(stringr,str_length)
importFrom(stringr,str_locate)
importFrom(stringr,str_locate_all)
importFrom(stringr,str_remove_all)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(stringr,str_sub)
importFrom(stringr,str_trim)
importFrom(stringr,word)
importFrom(sunburstR,sunburst)
importFrom(sunburstR,sund2b)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(tidyr,drop_na)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,replace_na)
importFrom(tidyr,separate)
importFrom(tidyr,unite)
importFrom(utils,combn)
importFrom(viridis,scale_fill_viridis)
importFrom(visNetwork,visEdges)
importFrom(visNetwork,visGroups)
importFrom(visNetwork,visIgraph)
importFrom(visNetwork,visIgraphLayout)
importFrom(visNetwork,visLegend)
importFrom(visNetwork,visNetwork)
importFrom(visNetwork,visOptions)
importFrom(wordcloud,wordcloud)
importFrom(yaml,read_yaml)
importFrom(yaml,write_yaml)