NAMESPACE

# Generated by roxygen2: do not edit by hand

export("%>%")
export("marker_table<-")
export(abundances)
export(aggregate_taxa)
export(arrange)
export(calculate_MeanRank_abundance)
export(calculate_geometricmean_abundance)
export(calculate_mean_abundance)
export(calculate_median_abundance)
export(calculate_occurrence_taxa)
export(confounder)
export(count)
export(distinct)
export(filter)
export(filter_abundance)
export(get_GUniFrac)
export(get_alphaindex)
export(group_by)
export(import_SE)
export(import_biom)
export(import_dada2)
export(import_mothur)
export(import_qiime)
export(import_qiime2)
export(impute_abundance)
export(insertCol)
export(insertRow)
export(lag)
export(left_join)
export(marker_table)
export(microbiomeMarker)
export(mutate)
export(nmarker)
export(norm_clr)
export(norm_cpm)
export(norm_css)
export(norm_rarefy)
export(norm_rle)
export(norm_tmm)
export(norm_tss)
export(nsamples)
export(ntaxa)
export(otu_table)
export(otu_table2metagenomeSeq)
export(phyloseq2DESeq2)
export(phyloseq2edgeR)
export(phyloseq2metagenomeSeq)
export(plot_ord)
export(plot_volcano)
export(postHocTest)
export(pull)
export(rename)
export(run_ANOSIM)
export(run_CI)
export(run_MANTEL)
export(run_MRPP)
export(run_OddRatio)
export(run_PERMANOVA)
export(run_STDERR)
export(run_aldex)
export(run_ancom)
export(run_ancombc)
export(run_betadisper)
export(run_deseq2)
export(run_distance)
export(run_edger)
export(run_group.CI)
export(run_group.STDERR)
export(run_lefse)
export(run_limma_voom)
export(run_marker)
export(run_metabolomeDA)
export(run_metagenomeseq)
export(run_ord)
export(run_simple_stat)
export(run_sl)
export(run_summarySE)
export(run_test_multiple_groups)
export(run_test_two_groups)
export(sample_data)
export(sample_names)
export(scale_variables)
export(select)
export(slice)
export(subset_marker)
export(summarize_taxa)
export(tax_table)
export(taxa_names)
export(transform_abundances)
export(trim_prevalence)
export(ungroup)
exportClasses(marker_table)
exportClasses(microbiomeMarker)
exportClasses(postHocTest)
exportMethods("[")
exportMethods(normalize)
exportMethods(nsamples)
exportMethods(ntaxa)
exportMethods(otu_table)
exportMethods(sample_data)
exportMethods(sample_names)
exportMethods(show)
exportMethods(tax_table)
exportMethods(taxa_names)
import(SummarizedExperiment)
import(dplyr)
import(ggplot2)
import(phyloseq)
import(stats)
import(vegan)
importClassesFrom(IRanges,DataFrameList)
importClassesFrom(phyloseq,otu_table)
importClassesFrom(phyloseq,phyloseq)
importClassesFrom(phyloseq,taxonomyTable)
importFrom(ANCOMBC,ancombc)
importFrom(Biobase,"pData<-")
importFrom(Biobase,AnnotatedDataFrame)
importFrom(Biobase,pData)
importFrom(DESeq2,"dispersions<-")
importFrom(MASS,cov.trob)
importFrom(RColorBrewer,brewer.pal)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(biomformat,biom_data)
importFrom(biomformat,read_biom)
importFrom(dplyr,"%>%")
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,count)
importFrom(dplyr,distinct)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_split)
importFrom(dplyr,inner_join)
importFrom(dplyr,lag)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,ungroup)
importFrom(magrittr,"%>%")
importFrom(metagenomeSeq,"normFactors<-")
importFrom(metagenomeSeq,MRcounts)
importFrom(metagenomeSeq,cumNorm)
importFrom(metagenomeSeq,cumNormStatFast)
importFrom(metagenomeSeq,newMRexperiment)
importFrom(phyloseq,"otu_table<-")
importFrom(phyloseq,"sample_data<-")
importFrom(phyloseq,"tax_table<-")
importFrom(phyloseq,"taxa_are_rows<-")
importFrom(phyloseq,"taxa_names<-")
importFrom(phyloseq,import_biom)
importFrom(phyloseq,import_mothur)
importFrom(phyloseq,import_qiime)
importFrom(phyloseq,merge_phyloseq)
importFrom(phyloseq,nsamples)
importFrom(phyloseq,ntaxa)
importFrom(phyloseq,otu_table)
importFrom(phyloseq,prune_samples)
importFrom(phyloseq,rank_names)
importFrom(phyloseq,rarefy_even_depth)
importFrom(phyloseq,read_tree)
importFrom(phyloseq,sample_data)
importFrom(phyloseq,sample_names)
importFrom(phyloseq,sample_sums)
importFrom(phyloseq,t)
importFrom(phyloseq,tax_glom)
importFrom(phyloseq,tax_table)
importFrom(phyloseq,taxa_are_rows)
importFrom(phyloseq,taxa_names)
importFrom(phyloseq,transform_sample_counts)
importFrom(purrr,map)
importFrom(purrr,map_dbl)
importFrom(purrr,map_df)
importFrom(purrr,pmap_chr)
importFrom(purrr,pmap_dbl)
importFrom(stats,anova)
importFrom(stats,aov)
importFrom(stats,as.dist)
importFrom(stats,coef)
importFrom(stats,dnorm)
importFrom(stats,drop1)
importFrom(stats,fisher.test)
importFrom(stats,formula)
importFrom(stats,glm)
importFrom(stats,kruskal.test)
importFrom(stats,lm)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,psignrank)
importFrom(stats,pt)
importFrom(stats,pwilcox)
importFrom(stats,quantile)
importFrom(stats,relevel)
importFrom(stats,residuals)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(stats,wilcox.test)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,separate)
importFrom(vegan,adonis)
importFrom(vegan,anosim)
importFrom(vegan,betadisper)
importFrom(vegan,cca)
importFrom(vegan,mantel)
importFrom(vegan,mantel.partial)
importFrom(vegan,mrpp)
importFrom(vegan,permutest)
importFrom(vegan,vegdist)
importFrom(yaml,read_yaml)
importMethodsFrom(BiocGenerics,"sizeFactors<-")
importMethodsFrom(BiocGenerics,counts)
importMethodsFrom(BiocGenerics,normalize)
importMethodsFrom(S4Vectors,mcols)
importMethodsFrom(phyloseq,"otu_table<-")
importMethodsFrom(phyloseq,nsamples)
importMethodsFrom(phyloseq,ntaxa)
importMethodsFrom(phyloseq,otu_table)
importMethodsFrom(phyloseq,sample_data)
importMethodsFrom(phyloseq,sample_names)
importMethodsFrom(phyloseq,t)
importMethodsFrom(phyloseq,tax_table)
importMethodsFrom(phyloseq,taxa_names)