NAMESPACE

# Generated by roxygen2: do not edit by hand

export(Bartlett_test)
export(Bootstrap_phy_tree_with_cophenetic)
export(MG)
export(MG_shape)
export(Pre_processing_hashcodes)
export(Pre_processing_species)
export(Pre_processing_species_list)
export(RandomForest_selected_ASVs)
export(Shapiro_Wilk_test)
export(adjust_abundance_one_third)
export(adjusted_prevalence)
export(alluvial_plot)
export(calculate_list_average_scaling_factors)
export(calculate_spikeIn_factors)
export(calculate_spike_percentage)
export(calculate_spike_percentage_list)
export(calculate_summary_stats_table)
export(color_palette)
export(conclusion)
export(convert_to_absolute_counts)
export(create_directory)
export(detect_common_asvs_taxa)
export(gm_mean)
export(my_custom_theme)
export(normalization_set)
export(perform_and_visualize_DA)
export(plot_core_microbiome_custom)
export(plot_glommed_tree)
export(plot_tree_custom)
export(plot_tree_nj)
export(plot_tree_with_alignment)
export(proportion_adj)
export(random_subsample_WithReductionFactor)
export(randomsubsample_Trimmed_evenDepth)
export(regression_plot)
export(relativized_filtered_taxa)
export(ridge_plot_it)
export(set_nf)
export(summ_count_phyloseq)
export(summ_phyloseq_ASV_OTUID)
export(summ_phyloseq_sampleID)
export(taxa_barplot)
export(tidy_phyloseq)
export(transform_plot)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,writeXStringSet)
importFrom(DECIPHER,AlignSeqs)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,estimateSizeFactorsForMatrix)
importFrom(DESeq2,results)
importFrom(DESeq2,sizeFactors)
importFrom(RColorBrewer,brewer.pal)
importFrom(ape,boot.phylo)
importFrom(ape,cophenetic.phylo)
importFrom(ape,nj)
importFrom(ape,nodelabels)
importFrom(ape,plot.phylo)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,select_if)
importFrom(dplyr,slice_head)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_all)
importFrom(dplyr,summarize)
importFrom(dplyr,top_n)
importFrom(dplyr,ungroup)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,topTags)
importFrom(flextable,bold)
importFrom(flextable,color)
importFrom(flextable,flextable)
importFrom(flextable,font)
importFrom(flextable,fontsize)
importFrom(flextable,italic)
importFrom(flextable,save_as_docx)
importFrom(ggalluvial,geom_alluvium)
importFrom(ggalluvial,geom_stratum)
importFrom(ggalluvial,is_alluvia_form)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,after_stat)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_label)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_continuous)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggpubr,color_palette)
importFrom(ggpubr,stat_compare_means)
importFrom(ggpubr,stat_cor)
importFrom(ggpubr,stat_regline_equation)
importFrom(ggridges,geom_density_ridges2)
importFrom(ggtree,geom_text2)
importFrom(ggtree,geom_tiplab)
importFrom(ggtree,geom_tippoint)
importFrom(ggtree,ggtree)
importFrom(ggtree,msaplot)
importFrom(ggtree,theme_tree2)
importFrom(grDevices,rainbow)
importFrom(graphics,boxplot)
importFrom(graphics,mtext)
importFrom(grid,unit)
importFrom(limma,makeContrasts)
importFrom(magrittr,"%>%")
importFrom(matrixStats,rowMeans2)
importFrom(matrixStats,rowMedians)
importFrom(methods,is)
importFrom(microbiome,plot_core)
importFrom(microbiomeutilities,format_to_besthit)
importFrom(msa,msa)
importFrom(phangorn,dist.ml)
importFrom(phangorn,phyDat)
importFrom(phyloseq,"otu_table<-")
importFrom(phyloseq,"taxa_names<-")
importFrom(phyloseq,filter_taxa)
importFrom(phyloseq,merge_phyloseq)
importFrom(phyloseq,merge_taxa)
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,psmelt)
importFrom(phyloseq,rarefy_even_depth)
importFrom(phyloseq,refseq)
importFrom(phyloseq,sample_data)
importFrom(phyloseq,sample_names)
importFrom(phyloseq,sample_sums)
importFrom(phyloseq,subset_samples)
importFrom(phyloseq,subset_taxa)
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(randomForest,importance)
importFrom(randomForest,randomForest)
importFrom(rlang,sym)
importFrom(scales,label_scientific)
importFrom(speedyseq,tree_glom)
importFrom(stats,aov)
importFrom(stats,kruskal.test)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,reformulate)
importFrom(stats,resid)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,shapiro.test)
importFrom(stats,wilcox.test)
importFrom(tibble,as_tibble)
importFrom(utils,capture.output)
importFrom(utils,globalVariables)
importFrom(utils,install.packages)
importFrom(utils,write.csv)