AnalyzAIRR/NAMESPACE at master · i3-unit/AnalyzAIRR · GitHub

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# Generated by roxygen2: do not edit by hand

export(.safe_kruskal_pairwise)
export(.safe_wilcox)
export(.toDESeq2)
export(CalcDissimilarity)
export(Intervals)
export(RepSeqExp)
export(ShannonNorm)
export(chaoWor)
export(countFeatures)
export(diffExpGroup)
export(diffExpInd)
export(divLevel)
export(diversityIndices)
export(dropSamples)
export(filetype)
export(filterClones)
export(filterCount)
export(filterSequence)
export(formatSingleCell)
export(generalizedDiversity)
export(getPrivate)
export(getProductive)
export(getPublic)
export(getTopSequences)
export(getUnproductive)
export(iChao)
export(is.RepSeqExperiment)
export(mergeRepSeq)
export(named.contr.sum)
export(parseAIRRC)
export(parseImmunoseq)
export(parseMiXCR)
export(perturbationScore)
export(plotColors)
export(plotDiffExp)
export(plotDissHeatmap)
export(plotDissMDS)
export(plotDiversity)
export(plotGenDiversity)
export(plotGeneUsage)
export(plotIndGeneUsage)
export(plotIndIntervals)
export(plotIndMap)
export(plotIndStatistics)
export(plotIntervals)
export(plotPerturbationScore)
export(plotRankDistrib)
export(plotRarefaction)
export(plotScatter)
export(plotSpectratyping)
export(plotSpectratypingV)
export(plotStatScatter)
export(plotStatistics)
export(plotVJusage)
export(plotVenn)
export(readAIRR)
export(readAIRRSet)
export(readFormatSet)
export(readInFormat)
export(readSingleCellSet)
export(sampleRepSeqExp)
export(theme_RepSeq)
exportClasses(RepSeqExperiment)
exportMethods("History<-")
exportMethods("[")
exportMethods("assay<-")
exportMethods("mData<-")
exportMethods("oData<-")
exportMethods(History)
exportMethods(assay)
exportMethods(mData)
exportMethods(oData)
import(ComplexHeatmap)
import(GGally)
import(RColorBrewer)
import(ade4)
import(data.table)
import(ggplot2)
import(ggprism)
import(ggpubr)
import(grDevices)
import(graphics)
import(methods)
import(naturalsort)
import(packcircles)
import(parallel)
import(pbapply)
import(rstatix)
import(smplot2)
import(stringr)
import(tibble)
import(tidyverse)
import(utils)
import(vegan)
importFrom(R.utils,decompressFile)
importFrom(car,dataEllipse)
importFrom(circlize,chordDiagram)
importFrom(circlize,circos.text)
importFrom(circlize,circos.track)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(ggVennDiagram,ggVennDiagram)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(magrittr,"%>%")
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(stats,as.formula)
importFrom(stats,cmdscale)
importFrom(stats,cor.test)
importFrom(stats,frequency)
importFrom(stats,lag)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,sd)
importFrom(stats,var)
importFrom(testthat,test_that)