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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(add_taxa,Strata)
S3method(add_taxa,phylo)
S3method(children,Strata)
S3method(descendent_nodes,Strata)
S3method(descendent_nodes,phylo)
S3method(descendents,Strata)
S3method(descendents,phylo)
S3method(get_root,Strata)
S3method(get_root,phylo)
S3method(is_root,Strata)
S3method(is_root,phylo)
S3method(leafs,Strata)
S3method(leafs,phylo)
S3method(lineage,Strata)
S3method(lineage,phylo)
S3method(make_tree_relative_to,Strata)
S3method(make_tree_relative_to,phylo)
S3method(merge_phylo,Strata)
S3method(merge_phylo,phylo)
S3method(nleafs,Strata)
S3method(nleafs,phylo)
S3method(nodes,Strata)
S3method(nodes,phylo)
S3method(parent,Strata)
S3method(parent,phylo)
S3method(plot,CountMatrix)
S3method(plot,Strata)
S3method(print,Strata)
S3method(prune,Strata)
S3method(prune,phylo)
S3method(set_node_names,Strata)
S3method(set_node_names,phylo)
S3method(sister_trees,Strata)
S3method(sister_trees,phylo)
S3method(sisters,Strata)
S3method(sisters,phylo)
S3method(subtree,Strata)
S3method(subtree,phylo)
S3method(t,CountMatrix)
S3method(tree_names,Strata)
S3method(tree_names,phylo)
S3method(tree_size,Strata)
S3method(tree_size,phylo)
export(CountMatrix)
export(Strata)
export(add_organelle_proteins)
export(add_proteome_stats)
export(add_taxa)
export(children)
export(classify_by_adjusted_pvalue)
export(classify_by_evalue)
export(classify_by_pvalue)
export(constrict)
export(descendent_nodes)
export(descendents)
export(diverse_subtree)
export(edgelist_to_phylo)
export(extract_uniprot_id_from_fasta)
export(find_revenants)
export(get_besthit)
export(get_max_hit)
export(get_mrca_names)
export(get_phylostrata_map)
export(get_root)
export(is_root)
export(leafs)
export(lineage)
export(lineage_to_ancestor_tree)
export(lineages_to_phylo)
export(load_hittable)
export(make_blast_database)
export(make_jump_matrix)
export(make_matrix_from_two_strata)
export(make_significance_matrices)
export(make_tree_relative_to)
export(merge_besthits)
export(merge_phylo)
export(ncbi_ancestors)
export(ncbi_aunts)
export(ncbi_cousins)
export(ncbi_tree)
export(nleafs)
export(nodes)
export(normalize_matrix_by_col)
export(normalize_matrix_by_row)
export(organelle_table)
export(parent)
export(partial_id_to_name)
export(plot_heatmaps)
export(plot_phyloheatmap)
export(plot_proteome_lengths)
export(plot_proteome_stats)
export(proteome_report_table)
export(proteome_stats_table)
export(prune)
export(prune_phylostrata)
export(read_blast)
export(replace_branch)
export(run_blastp)
export(set_node_names)
export(sister_trees)
export(sisters)
export(sort_strata)
export(standardize_strata)
export(strata_apply)
export(strata_besthits)
export(strata_blast)
export(strata_convert)
export(strata_diamond)
export(strata_from_blast_dir)
export(strata_from_taxids)
export(strata_map)
export(strata_uniprot_pfam_map)
export(stratify)
export(subset_fasta)
export(subtree)
export(thin_fasta)
export(tree2edgelist)
export(tree_names)
export(tree_size)
export(uniprot_add_idmap)
export(uniprot_downstream_ids)
export(uniprot_fill_strata)
export(uniprot_map2pfam)
export(uniprot_organelle_ids)
export(uniprot_retrieve_proteome)
export(uniprot_retrieve_proteome_table)
export(uniprot_strata)
export(uniprot_weight_by_ref)
export(use_recommended_prokaryotes)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,plot)
importFrom(magrittr,"%>%")
importFrom(methods,new)
importFrom(rlang,.data)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,quantile)
importFrom(utils,head)
importFrom(utils,tail)