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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(GF)
export(NMF)
export(addGeneAbundance)
export(alleleStat)
export(alphaDiversityWithinSpecies)
export(anno_PATRIC_keywords)
export(anno_eggNOG_keywords)
export(calcGF)
export(changeColors)
export(check)
export(checkEGGNOG)
export(checkPATRIC)
export(checkPATRICSimple)
export(cnDiscretize)
export(combineGenes)
export(combineMaf)
export(combineSeqs)
export(compareGenes)
export(consensusSeq)
export(consensusSeqGeneral)
export(consensusSeqMIDAS1)
export(consensusSeqMIDAS2)
export(convertWideToMaf)
export(doAdonis)
export(doBoruta)
export(doGSEA)
export(doL0)
export(drawEGGNOG)
export(drawPATRIC)
export(exportInteractive)
export(filter)
export(fromHumann)
export(gene)
export(genomeHeatmap)
export(getAdonis)
export(getCl)
export(getFasta)
export(getGeneID)
export(getID)
export(getKOID)
export(getSNVID)
export(getSlot)
export(getTree)
export(getTreePlot)
export(inferAndPlotTree)
export(loadInStrain)
export(loadMIDAS)
export(loadMIDAS2)
export(loadmetaSNV)
export(obtainPositions)
export(pathwayWithFactor)
export(plotAbundanceWithinSpecies)
export(plotCirclize)
export(plotCoverage)
export(plotDist)
export(plotGSEA)
export(plotGenes)
export(plotHeatmap)
export(plotKEGGPathway)
export(plotMAF)
export(plotMAFHist)
export(plotPCA)
export(plotSNVInfo)
export(plotSNVSummary)
export(plotStackedBarPlot)
export(rankComponents)
export(returnGenes)
export(reverseAnnot)
export(scaler.NNLM)
export(setAnnotation)
export(setGroup)
export(setMap)
export(setMetadata)
export(setSNVID)
export(setSlot)
export(setTree)
export(siteFilter)
export(snv)
export(strainClusterHeatmap)
export(summariseAbundance)
export(summary)
exportMethods(check)
exportMethods(filter)
exportMethods(getAdonis)
exportMethods(getCl)
exportMethods(getFasta)
exportMethods(getGeneID)
exportMethods(getID)
exportMethods(getKOID)
exportMethods(getSNVID)
exportMethods(getSlot)
exportMethods(getTree)
exportMethods(getTreePlot)
exportMethods(setSNVID)
exportMethods(setSlot)
exportMethods(siteFilter)
exportMethods(summary)
import(BiocFileCache)
import(GetoptLong)
import(RColorBrewer)
import(RCurl)
import(ggplot2)
import(ggraph)
import(ggtree)
import(igraph)
import(methods)
importFrom(ComplexHeatmap,Heatmap)
importFrom(MKmisc,mod.t.test)
importFrom(NMF,nmf)
importFrom(NMF,nmfEstimateRank)
importFrom(circlize,CELL_META)
importFrom(circlize,circos.barplot)
importFrom(circlize,circos.clear)
importFrom(circlize,circos.initialize)
importFrom(circlize,circos.par)
importFrom(circlize,circos.points)
importFrom(circlize,circos.rect)
importFrom(circlize,circos.text)
importFrom(circlize,circos.track)
importFrom(data.table,fread)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,summarise)
importFrom(ggkegg,pathway)
importFrom(ggnewscale,new_scale_fill)
importFrom(ggplotify,as.ggplot)
importFrom(ggstar,geom_star)
importFrom(ggtreeExtra,geom_fruit)
importFrom(grDevices,colorRampPalette)
importFrom(phangorn,NJ)
importFrom(phangorn,dist.ml)
importFrom(phangorn,read.phyDat)
importFrom(scico,scale_color_scico)
importFrom(scico,scale_color_scico_d)
importFrom(scico,scale_fill_scico)
importFrom(scico,scale_fill_scico_d)
importFrom(stats,as.formula)
importFrom(stats,dist)
importFrom(stats,prcomp)
importFrom(tidygraph,"%E>%")
importFrom(tidygraph,"%N>%")
importFrom(utils,object.size)
importFrom(utils,read.table)
importFrom(vegan,adonis2)