# Generated by roxygen2: do not edit by hand

export(MG_shapes)
export(Pre_processing_hashcodes)
export(Pre_processing_species)
export(Pre_processing_species_list)
export(RandomForest_selected)
export(adjust_abundance_by_factor)
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_categorical_to_factors)
export(convert_phyloseq_to_tse)
export(convert_to_absolute_counts)
export(convert_tse_to_phyloseq)
export(create_directory)
export(degree_network)
export(detect_common_asvs_taxa)
export(extract_neighbors)
export(filter_and_split_abundance)
export(get_long_format_data)
export(get_otu_table)
export(get_phy_tree)
export(get_reference_seq)
export(get_sample_data)
export(get_sample_sums)
export(get_tax_table)
export(gm_mean)
export(imbalance_calculate_list_average_scaling_factors)
export(label)
export(load_graphml)
export(my_custom_theme)
export(node_level_metrics)
export(norm.DESeq)
export(normalization_set)
export(perform_and_visualize_DA)
export(plot_core_microbiome_custom)
export(plot_spikein_tree_diagnostic)
export(plotbar_abundance)
export(proportion_adj)
export(quadrant_plot)
export(random_subsample_WithReductionFactor)
export(randomsubsample_Trimmed_evenDepth)
export(regression_plot)
export(relativized_filtered_taxa)
export(remove_zero_negative_count_samples)
export(ridge_plot_it)
export(set_nf)
export(simulate_network_robustness)
export(summ_ASV_OTUID)
export(summ_count_phyloseq)
export(summ_phyloseq_sampleID)
export(taxa_barplot)
export(tidy_phyloseq_tse)
export(validate_spikein_clade)
export(weight_Network)
exportClasses(ExpData)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,readDNAStringSet)
importFrom(DECIPHER,AlignSeqs)
importFrom(DESeq2,"dispersions<-")
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,estimateDispersionsGeneEst)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,estimateSizeFactorsForMatrix)
importFrom(DESeq2,nbinomWaldTest)
importFrom(DESeq2,results)
importFrom(DESeq2,sizeFactors)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,colnames)
importFrom(SummarizedExperiment,mcols)
importFrom(SummarizedExperiment,rowData)
importFrom(TreeSummarizedExperiment,"referenceSeq<-")
importFrom(TreeSummarizedExperiment,TreeSummarizedExperiment)
importFrom(TreeSummarizedExperiment,referenceSeq)
importFrom(TreeSummarizedExperiment,rowTree)
importFrom(ape,as.phylo)
importFrom(ape,boot.phylo)
importFrom(ape,cophenetic.phylo)
importFrom(ape,drop.tip)
importFrom(ape,is.monophyletic)
importFrom(ape,is.rooted)
importFrom(ape,ladderize)
importFrom(ape,nj)
importFrom(ape,nodelabels)
importFrom(ape,plot.phylo)
importFrom(ape,prop.clades)
importFrom(ape,tiplabels)
importFrom(ape,write.tree)
importFrom(data.table,":=")
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,case_when)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,if_else)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_at)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,rename_with)
importFrom(dplyr,select)
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(dplyr,where)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,topTags)
importFrom(flextable,align)
importFrom(flextable,autofit)
importFrom(flextable,bg)
importFrom(flextable,bold)
importFrom(flextable,color)
importFrom(flextable,flextable)
importFrom(flextable,font)
importFrom(flextable,fontsize)
importFrom(flextable,italic)
importFrom(flextable,save_as_docx)
importFrom(flextable,set_caption)
importFrom(flextable,theme_vanilla)
importFrom(flextable,width)
importFrom(ggalluvial,geom_alluvium)
importFrom(ggalluvial,geom_stratum)
importFrom(ggalluvial,is_alluvia_form)
importFrom(ggnewscale,new_scale_fill)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,after_stat)
importFrom(ggplot2,coord_flip)
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_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_label)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_linerange)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,scale_alpha_continuous)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_color_viridis_c)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_fill_viridis_d)
importFrom(ggplot2,scale_size_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggpubr,color_palette)
importFrom(ggpubr,stat_cor)
importFrom(ggpubr,stat_regline_equation)
importFrom(ggraph,create_layout)
importFrom(ggraph,geom_edge_link)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,ggraph)
importFrom(ggraph,scale_edge_colour_manual)
importFrom(ggrepel,geom_text_repel)
importFrom(ggridges,geom_density_ridges2)
importFrom(ggstar,geom_star)
importFrom(ggtree,geom_text2)
importFrom(ggtree,geom_tiplab)
importFrom(ggtree,geom_tippoint)
importFrom(ggtree,ggtree)
importFrom(ggtree,theme_tree2)
importFrom(ggtreeExtra,geom_fruit)
importFrom(grDevices,col2rgb)
importFrom(grDevices,dev.new)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rainbow)
importFrom(grDevices,rgb)
importFrom(graphics,boxplot)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,mtext)
importFrom(grid,unit)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,betweenness)
importFrom(igraph,closeness)
importFrom(igraph,cluster_fast_greedy)
importFrom(igraph,cluster_louvain)
importFrom(igraph,components)
importFrom(igraph,constraint)
importFrom(igraph,coreness)
importFrom(igraph,degree)
importFrom(igraph,delete_vertex_attr)
importFrom(igraph,delete_vertices)
importFrom(igraph,diameter)
importFrom(igraph,distances)
importFrom(igraph,ecount)
importFrom(igraph,edge_density)
importFrom(igraph,eigen_centrality)
importFrom(igraph,induced_subgraph)
importFrom(igraph,is_connected)
importFrom(igraph,is_weighted)
importFrom(igraph,mean_distance)
importFrom(igraph,membership)
importFrom(igraph,modularity)
importFrom(igraph,neighbors)
importFrom(igraph,page_rank)
importFrom(igraph,read_graph)
importFrom(igraph,set_vertex_attr)
importFrom(igraph,strength)
importFrom(igraph,transitivity)
importFrom(igraph,vcount)
importFrom(igraph,vertex_attr_names)
importFrom(limma,makeContrasts)
importFrom(matrixStats,rowMeans2)
importFrom(matrixStats,rowMedians)
importFrom(methods,is)
importFrom(microbiome,meta)
importFrom(microbiome,plot_core)
importFrom(msa,msa)
importFrom(msa,msaConvert)
importFrom(officer,docx_summary)
importFrom(officer,read_docx)
importFrom(patchwork,wrap_plots)
importFrom(phangorn,bootstrap.phyDat)
importFrom(phangorn,dist.ml)
importFrom(phangorn,phyDat)
importFrom(phyloseq,"otu_table<-")
importFrom(phyloseq,"tax_table<-")
importFrom(phyloseq,"taxa_names<-")
importFrom(phyloseq,filter_taxa)
importFrom(phyloseq,merge_phyloseq)
importFrom(phyloseq,merge_taxa)
importFrom(phyloseq,nsamples)
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_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(reshape2,melt)
importFrom(rlang,as_name)
importFrom(rlang,sym)
importFrom(scales,label_scientific)
importFrom(scales,rescale)
importFrom(stats,aggregate)
importFrom(stats,as.formula)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,reformulate)
importFrom(stats,relevel)
importFrom(stats,reorder)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,wilcox.test)
importFrom(tibble,as_tibble)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(utils,capture.output)
importFrom(utils,globalVariables)
importFrom(utils,install.packages)
importFrom(utils,write.csv)
importFrom(xml2,read_xml)
importFrom(xml2,write_xml)
importFrom(xml2,xml_attr)
importFrom(xml2,xml_find_all)
importFrom(xml2,xml_remove)
importFrom(xml2,xml_set_attr)
