# Generated by roxygen2: do not edit by hand

export(CAT)
export(DA_ALDEx2)
export(DA_ANCOM)
export(DA_DESeq2)
export(DA_MAST)
export(DA_Maaslin2)
export(DA_NOISeq)
export(DA_Seurat)
export(DA_ZicoSeq)
export(DA_basic)
export(DA_corncob)
export(DA_dearseq)
export(DA_edgeR)
export(DA_limma)
export(DA_linda)
export(DA_maaslin3)
export(DA_metagenomeSeq)
export(DA_mixMC)
export(RMSE)
export(addKnowledge)
export(areaCAT)
export(checkNormalization)
export(createColors)
export(createConcordance)
export(createEnrichment)
export(createMocks)
export(createPositives)
export(createSplits)
export(createTIEC)
export(enrichmentTest)
export(extractDA)
export(extractStatistics)
export(fitDM)
export(fitHURDLE)
export(fitModels)
export(fitNB)
export(fitZIG)
export(fitZINB)
export(getDA)
export(getPositives)
export(getStatistics)
export(get_counts_metadata)
export(iterative_ordering)
export(meanDifferences)
export(norm_CSS)
export(norm_DESeq2)
export(norm_TSS)
export(norm_edgeR)
export(plotConcordance)
export(plotContingency)
export(plotEnrichment)
export(plotFDR)
export(plotFPR)
export(plotKS)
export(plotLogP)
export(plotMD)
export(plotMutualFindings)
export(plotPositives)
export(plotQQ)
export(plotRMSE)
export(prepareObserved)
export(runDA)
export(runMocks)
export(runNormalizations)
export(runSplits)
export(setNormalizations)
export(set_ALDEx2)
export(set_ANCOM)
export(set_DESeq2)
export(set_MAST)
export(set_Maaslin2)
export(set_NOISeq)
export(set_Seurat)
export(set_ZicoSeq)
export(set_basic)
export(set_corncob)
export(set_dearseq)
export(set_edgeR)
export(set_limma)
export(set_linda)
export(set_maaslin3)
export(set_metagenomeSeq)
export(set_mixMC)
export(weights_ZINB)
import(BiocParallel)
import(ggplot2)
import(methods)
importFrom(ALDEx2,aldex)
importFrom(ANCOMBC,ancom)
importFrom(ANCOMBC,ancombc2)
importFrom(BiocParallel,SerialParam)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,dispersions)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,results)
importFrom(DESeq2,sizeFactors)
importFrom(GUniFrac,ZicoSeq)
importFrom(MAST,FromMatrix)
importFrom(MAST,invlogit)
importFrom(MAST,summary)
importFrom(MAST,zlm)
importFrom(MGLM,MGLMreg)
importFrom(Maaslin2,Maaslin2)
importFrom(MicrobiomeStat,linda)
importFrom(NOISeq,noiseqbio)
importFrom(RColorBrewer,brewer.pal)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(Seurat,AddMetaData)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,FindMarkers)
importFrom(Seurat,FindVariableFeatures)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,NormalizeData)
importFrom(Seurat,ScaleData)
importFrom(Seurat,SetAssayData)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(TreeSummarizedExperiment,TreeSummarizedExperiment)
importFrom(corncob,differentialTest)
importFrom(cowplot,plot_grid)
importFrom(dearseq,dear_seq)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,estimateGLMRobustDisp)
importFrom(edgeR,getCounts)
importFrom(edgeR,getDispersion)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(ggdendro,dendro_data)
importFrom(ggdendro,label)
importFrom(ggridges,geom_density_ridges2)
importFrom(ggridges,position_raincloud)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,abline)
importFrom(graphics,plot)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(lme4,findbars)
importFrom(lme4,lmerControl)
importFrom(maaslin3,maaslin3)
importFrom(metagenomeSeq,MRfulltable)
importFrom(metagenomeSeq,cumNorm)
importFrom(metagenomeSeq,cumNormStat)
importFrom(metagenomeSeq,fitFeatureModel)
importFrom(metagenomeSeq,fitZig)
importFrom(metagenomeSeq,newMRexperiment)
importFrom(metagenomeSeq,normFactors)
importFrom(metagenomeSeq,zigControl)
importFrom(mixOmics,perf)
importFrom(mixOmics,plotLoadings)
importFrom(mixOmics,splsda)
importFrom(mixOmics,tune.splsda)
importFrom(phyloseq,filter_taxa)
importFrom(phyloseq,otu_table)
importFrom(phyloseq,phyloseq)
importFrom(phyloseq,phyloseq_to_metagenomeSeq)
importFrom(phyloseq,prune_samples)
importFrom(phyloseq,sample_data)
importFrom(phyloseq,sample_names)
importFrom(phyloseq,taxa_are_rows)
importFrom(phyloseq,taxa_names)
importFrom(plyr,ddply)
importFrom(plyr,is.formula)
importFrom(plyr,join)
importFrom(plyr,ldply)
importFrom(plyr,llply)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(stats,as.dist)
importFrom(stats,as.formula)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,ks.test)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,runif)
importFrom(stats,weights)
importFrom(stats4,coef)
importFrom(tidytext,reorder_within)
importFrom(tidytext,scale_x_reordered)
importFrom(utils,capture.output)
importFrom(zinbwave,computeObservationalWeights)
importFrom(zinbwave,getMu)
importFrom(zinbwave,getPhi)
importFrom(zinbwave,getPi)
importFrom(zinbwave,zinbFit)
