# Generated by roxygen2: do not edit by hand

S3method(ggplot2::ggplot_add,reorder_distinct_colors_spec)
S3method(unique_or_na,default)
S3method(unique_or_na,factor)
export(LCBD_pq)
export(SRS_curve_pq)
export(accu_plot)
export(accu_plot_balanced_modality)
export(accu_samp_threshold)
export(add_blast_info)
export(add_dna_to_phyloseq)
export(add_funguild_info)
export(add_info_to_sam_data)
export(add_new_taxonomy_pq)
export(adonis_phyloseq)
export(adonis_pq)
export(adonis_rarperm_pq)
export(aldex_pq)
export(all_object_size)
export(ancombc_pq)
export(are_modality_even_depth)
export(as_binary_otu_table)
export(assign_blastn)
export(assign_dada2)
export(assign_idtaxa)
export(assign_mmseqs2)
export(assign_sintax)
export(assign_vsearch_lca)
export(asv2otu)
export(biplot_physeq)
export(biplot_pq)
export(blast_pq)
export(blast_to_derep)
export(blast_to_phyloseq)
export(build_phytree_pq)
export(chimera_detection_vs)
export(chimera_removal_vs)
export(circle_pq)
export(clean_physeq)
export(clean_pq)
export(compare_pairs_pq)
export(count_seq)
export(css_pq)
export(cutadapt_remove_primers)
export(diff_fct_diff_class)
export(dist_bycol)
export(dist_pos_control)
export(distri_1_taxa)
export(divent_hill_matrix_pq)
export(fac2col)
export(filt_taxa_pq)
export(filt_taxa_wo_NA)
export(filter_asv_blast)
export(filter_taxa_blast)
export(filter_trim)
export(find_mmseqs2)
export(find_vsearch)
export(format2dada2)
export(format2dada2_species)
export(format2sintax)
export(formattable_pq)
export(funguild_assign)
export(funky_color)
export(get_file_extension)
export(get_funguild_db)
export(ggVenn_phyloseq)
export(ggaluv_pq)
export(ggbetween_pq)
export(ggscatt_pq)
export(ggvenn_pq)
export(glmutli_pq)
export(gmpr_pq)
export(graph_test_pq)
export(hill_acc_pq)
export(hill_bar_pq)
export(hill_curves_pq)
export(hill_phyloseq)
export(hill_pq)
export(hill_test_rarperm_pq)
export(hill_tuckey_phyloseq)
export(hill_tuckey_pq)
export(iNEXT_pq)
export(install_mmseqs2)
export(install_vsearch)
export(is_cutadapt_installed)
export(is_falco_installed)
export(is_krona_installed)
export(is_mmseqs2_installed)
export(is_mumu_installed)
export(is_swarm_installed)
export(is_vsearch_installed)
export(krona)
export(learn_idtaxa)
export(lefser_pq)
export(list_fastq_files)
export(lulu)
export(lulu_phyloseq)
export(lulu_pq)
export(mcknight_residuals_pq)
export(merge_krona)
export(merge_samples2)
export(merge_taxa_vec)
export(mmseqs2_clustering)
export(multi_biplot_pq)
export(multipatt_pq)
export(multiplot)
export(multitax_bar_pq)
export(mumu_pq)
export(no_legend)
export(normalize_prop_pq)
export(otu_circle)
export(perc)
export(phyloseq_to_edgeR)
export(physeq_graph_test)
export(physeq_or_string_to_dna)
export(plot_LCBD_pq)
export(plot_SCBD_pq)
export(plot_ancombc_pq)
export(plot_complexity_pq)
export(plot_deseq2_phyloseq)
export(plot_deseq2_pq)
export(plot_edgeR_phyloseq)
export(plot_edgeR_pq)
export(plot_guild_pq)
export(plot_mt)
export(plot_ordination_pq)
export(plot_refseq_extremity_pq)
export(plot_refseq_pq)
export(plot_seq_ratio_pq)
export(plot_tax_pq)
export(plot_tsne_pq)
export(plot_var_part_pq)
export(postcluster_pq)
export(profile_hill_pq)
export(psmelt_samples_pq)
export(rarefy_even_depth_pq)
export(rarefy_pq)
export(rarefy_sample_count_by_modality)
export(read_phyloseq)
export(read_pq)
export(rename_samples)
export(rename_samples_otu_table)
export(reorder_distinct_colors)
export(reorder_taxa_pq)
export(resolve_vector_ranks)
export(ridges_pq)
export(ridges_sam_pq)
export(rotl_pq)
export(sam_data_matching_names)
export(sample_data_with_new_names)
export(sankey_phyloseq)
export(sankey_pq)
export(save_pq)
export(search_exact_seq_pq)
export(select_one_sample)
export(signif_ancombc)
export(simplify_taxo)
export(srs_pq)
export(subsample_fastq)
export(subset_samples_pq)
export(subset_taxa_pq)
export(subset_taxa_tax_control)
export(summary_plot_phyloseq)
export(summary_plot_pq)
export(swarm_clustering)
export(tax_bar_pq)
export(tax_datatable)
export(taxa_as_columns)
export(taxa_as_rows)
export(taxa_only_in_one_level)
export(tbl_sum_samdata)
export(tbl_sum_taxtable)
export(tmm_pq)
export(track_wkflow)
export(track_wkflow_samples)
export(transform_pq)
export(transp)
export(treemap_pq)
export(tsne_pq)
export(umap_pq)
export(unique_or_na)
export(unwanted_tax_patterns)
export(upset_pq)
export(upset_test_pq)
export(var_par_pq)
export(var_par_rarperm_pq)
export(venn_phyloseq)
export(venn_pq)
export(verify_pq)
export(verify_tax_table)
export(vs_search_global)
export(vsearch_clustering)
export(vst_pq)
export(write_phyloseq)
export(write_pq)
import(dplyr)
import(ggplot2)
import(phyloseq)
importFrom(XVector,subseq)
importFrom(divent,accum_hill)
importFrom(divent,div_hill)
importFrom(divent,ent_shannon)
importFrom(divent,ent_simpson)
importFrom(divent,profile_hill)
importFrom(grDevices,col2rgb)
importFrom(grDevices,convertColor)
importFrom(lifecycle,deprecated)
importFrom(rlang,"%||%")
importFrom(rlang,.data)
importFrom(stats,anova)
importFrom(stats,as.formula)
importFrom(stats,ave)
importFrom(stats,dist)
importFrom(stats,kruskal.test)
importFrom(stats,na.exclude)
importFrom(stats,na.omit)
importFrom(stats,quantile)
importFrom(stats,reformulate)
importFrom(stats,reorder)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,terms)
importFrom(utils,object.size)
importFrom(utils,read.csv)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
