/
NAMESPACE
229 lines (228 loc) · 6.24 KB
/
NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(plot,compareDA)
S3method(summary,compareDA)
export("%>%")
export("marker_table<-")
export(abundances)
export(aggregate_taxa)
export(compare_DA)
export(confounder)
export(extract_posthoc_res)
export(import_biom)
export(import_dada2)
export(import_mothur)
export(import_picrust2)
export(import_qiime)
export(import_qiime2)
export(marker_table)
export(microbiomeMarker)
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_abundance)
export(plot_cladogram)
export(plot_ef_bar)
export(plot_ef_dot)
export(plot_heatmap)
export(plot_postHocTest)
export(plot_sl_roc)
export(postHocTest)
export(run_aldex)
export(run_ancom)
export(run_ancombc)
export(run_deseq2)
export(run_edger)
export(run_lefse)
export(run_limma_voom)
export(run_marker)
export(run_metagenomeseq)
export(run_posthoc_test)
export(run_simple_stat)
export(run_sl)
export(run_test_multiple_groups)
export(run_test_two_groups)
export(sample_data)
export(sample_names)
export(subset_marker)
export(summarize_taxa)
export(tax_table)
export(taxa_names)
export(transform_abundances)
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)
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(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(DESeq2,"dispersions<-")
importFrom(IRanges,DataFrameList)
importFrom(biomformat,biom_data)
importFrom(biomformat,read_biom)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,desc)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_modify)
importFrom(dplyr,group_split)
importFrom(dplyr,mutate)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_equal)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_axis)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labeller)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggtree,geom_cladelabel)
importFrom(ggtree,geom_hilight)
importFrom(ggtree,geom_point2)
importFrom(ggtree,ggtree)
importFrom(magrittr,"%>%")
importFrom(metagenomeSeq,"normFactors<-")
importFrom(metagenomeSeq,MRcounts)
importFrom(metagenomeSeq,cumNorm)
importFrom(metagenomeSeq,cumNormStatFast)
importFrom(metagenomeSeq,newMRexperiment)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(phyloseq,"otu_table<-")
importFrom(phyloseq,"sample_data<-")
importFrom(phyloseq,"tax_table<-")
importFrom(phyloseq,"taxa_are_rows<-")
importFrom(phyloseq,"taxa_names<-")
importFrom(phyloseq,`otu_table<-`)
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,phy_tree)
importFrom(phyloseq,phyloseq)
importFrom(phyloseq,prune_samples)
importFrom(phyloseq,prune_taxa)
importFrom(phyloseq,rank_names)
importFrom(phyloseq,rarefy_even_depth)
importFrom(phyloseq,read_tree)
importFrom(phyloseq,refseq)
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,taxa_sums)
importFrom(phyloseq,transform_sample_counts)
importFrom(plotROC,calc_auc)
importFrom(plotROC,geom_roc)
importFrom(plotROC,style_roc)
importFrom(purrr,map_dbl)
importFrom(purrr,pmap_chr)
importFrom(purrr,pmap_dbl)
importFrom(rlang,.data)
importFrom(stats,TukeyHSD)
importFrom(stats,anova)
importFrom(stats,aov)
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,median)
importFrom(stats,model.matrix)
importFrom(stats,model.tables)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pairwise.table)
importFrom(stats,pf)
importFrom(stats,pnorm)
importFrom(stats,psignrank)
importFrom(stats,pt)
importFrom(stats,ptukey)
importFrom(stats,pwilcox)
importFrom(stats,qf)
importFrom(stats,qtukey)
importFrom(stats,quantile)
importFrom(stats,relevel)
importFrom(stats,residuals)
importFrom(stats,sd)
importFrom(stats,var)
importFrom(stats,wilcox.test)
importFrom(tidytree,treedata)
importFrom(utils,read.delim)
importFrom(vegan,cca)
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)