API for arendsee/phylostratr
Analyze phylostratigraphic data
| Global functions | |
|---|---|
| .algo1 | Source code |
| .blastdb_exists | Source code |
| .check_type | Source code |
| .evalue2pvalue | Source code |
| .filenames_to_phylo | Source code |
| .fmap | Source code |
| .identity | Source code |
| .name | Source code |
| .strata | Source code |
| .validate_table | Source code |
| CountMatrix | Man page Source code |
| Strata | Man page Source code |
| access_cache | Source code |
| add_organelle_proteins | Man page Source code |
| add_proteome_stats | Man page Source code |
| add_taxa | Man page Source code |
| add_taxa.Strata | Man page Source code |
| add_taxa.phylo | Man page Source code |
| arabidopsis | Man page |
| arabidopsis_strata | Man page |
| atree | Man page |
| bind.tip | Source code |
| check_focal_species | Source code |
| check_hit_table | Source code |
| check_noise | Source code |
| children | Man page Source code |
| children.Strata | Man page Source code |
| children.phylo | Source code |
| classify_by_adjusted_pvalue | Man page Source code |
| classify_by_evalue | Man page Source code |
| classify_by_pvalue | Man page Source code |
| clean_phyid | Man page Source code |
| constrict | Man page Source code |
| data_tree_to_result_tree | Man page Source code |
| descendent_nodes | Man page Source code |
| descendent_nodes.Strata | Man page Source code |
| descendent_nodes.phylo | Man page Source code |
| descendents | Man page Source code |
| descendents.Strata | Man page Source code |
| descendents.phylo | Man page Source code |
| diverse_subtree | Man page Source code |
| edgelist_to_phylo | Man page Source code |
| eval_bins | Source code |
| extract_uniprot_id_from_fasta | Man page Source code |
| find_revenants | Man page Source code |
| find_skip_runs | Source code |
| find_strange | Source code |
| get_besthit | Man page Source code |
| get_max_hit | Man page Source code |
| get_mrca_names | Man page Source code |
| get_phylostrata_map | Man page |
| get_root | Man page Source code |
| get_root.Strata | Man page Source code |
| get_root.phylo | Man page Source code |
| has_header | Man page Source code |
| homolog_tree_to_phylostrata | Man page Source code |
| is_root | Man page Source code |
| is_root.Strata | Man page Source code |
| is_root.phylo | Man page Source code |
| is_valid_strata | Man page Source code |
| leafs | Man page Source code |
| leafs.Strata | Man page Source code |
| leafs.phylo | Man page Source code |
| lineage | Man page Source code |
| lineage.Strata | Man page Source code |
| lineage.phylo | Man page Source code |
| lineage_to_ancestor_tree | Man page Source code |
| lineages_to_phylo | Man page Source code |
| list_content | Source code |
| load_hittable | Man page Source code |
| make_blast_database | Man page Source code |
| make_diamond_database | Man page Source code |
| make_hmmscan_filter | Source code |
| make_jump_matrix | Man page Source code |
| make_matrix_from_two_strata | Man page Source code |
| make_noise | Source code |
| make_significance_matrices | Man page Source code |
| make_tree_relative_to | Man page Source code |
| make_tree_relative_to.Strata | Man page Source code |
| make_tree_relative_to.phylo | Man page Source code |
| map_ids | Man page Source code |
| map_node_label | Man page Source code |
| maybe_message | Source code |
| merge_besthits | Man page Source code |
| merge_pfam | Source code |
| merge_phylo | Man page Source code |
| merge_phylo.Strata | Man page Source code |
| merge_phylo.phylo | Man page Source code |
| ncbi_ancestors | Man page Source code |
| ncbi_aunts | Man page Source code |
| ncbi_cousins | Man page Source code |
| ncbi_tree | Man page Source code |
| nleafs | Man page Source code |
| nleafs.Strata | Man page Source code |
| nleafs.phylo | Man page Source code |
| nodes | Man page Source code |
| nodes.Strata | Man page Source code |
| nodes.phylo | Man page Source code |
| normalize_matrix_by_col | Man page Source code |
| normalize_matrix_by_row | Man page Source code |
| organelle_table | Man page Source code |
| parent | Man page Source code |
| parent.Strata | Man page Source code |
| parent.phylo | Man page Source code |
| partial_id_to_name | Man page |
| phylostratr | Man page |
| phylostratr-package | Man page |
| plot.CountMatrix | Man page Source code |
| plot.Strata | Man page Source code |
| plot_heatmaps | Man page Source code |
| plot_one_phyloheatmap | Source code |
| plot_phyloheatmap | Man page Source code |
| plot_proteome_lengths | Man page Source code |
| plot_proteome_stats | Man page Source code |
| print.Strata | Man page Source code |
| proteome_report_table | Man page Source code |
| proteome_stats_table | Man page Source code |
| prune | Man page Source code |
| prune.Strata | Man page Source code |
| prune.phylo | Man page Source code |
| prune_phylostrata | Man page |
| query_sparql | Man page Source code |
| read_blast | Man page Source code |
| rename_species | Man page |
| replace_branch | Man page Source code |
| result_tree_to_homolog_tree | Man page Source code |
| result_tree_to_pvalue_tree | Man page Source code |
| run_blastp | Man page Source code |
| run_diamond_blastp | Man page Source code |
| run_hmmscan | Man page Source code |
| saccharomyces | Man page |
| set_node_names | Man page Source code |
| set_node_names.Strata | Man page Source code |
| set_node_names.phylo | Man page Source code |
| sister_trees | Man page Source code |
| sister_trees.Strata | Man page Source code |
| sister_trees.phylo | Man page Source code |
| sisters | Man page Source code |
| sisters.Strata | Man page Source code |
| sisters.phylo | Man page Source code |
| sort_strata | Man page |
| species_to_species_tree | Man page Source code |
| species_tree_to_data_tree | Man page Source code |
| standardize_strata | Man page |
| strata_apply | Man page Source code |
| strata_besthits | Man page Source code |
| strata_blast | Man page Source code |
| strata_convert | Man page |
| strata_diamond | Man page Source code |
| strata_from_blast_dir | Man page Source code |
| strata_from_taxids | Man page |
| strata_hmmscan | Source code |
| strata_load_hmmscan | Source code |
| strata_map | Man page Source code |
| strata_uniprot_pfam_map | Man page Source code |
| stratify | Man page |
| stratify_by_pfam_domain | Source code |
| subset_fasta | Man page Source code |
| subtree | Man page Source code |
| subtree.Strata | Man page Source code |
| subtree.phylo | Man page Source code |
| t.CountMatrix | Man page Source code |
| thin_fasta | Man page Source code |
| tree2edgelist | Man page Source code |
| tree_names | Man page Source code |
| tree_names.Strata | Man page Source code |
| tree_names.phylo | Man page Source code |
| tree_size | Man page Source code |
| tree_size.Strata | Man page Source code |
| tree_size.phylo | Man page Source code |
| tuplify | Source code |
| uniprot_add_idmap | Man page Source code |
| uniprot_downstream_ids | Man page Source code |
| uniprot_fill_strata | Man page Source code |
| uniprot_map2pfam | Man page Source code |
| uniprot_organelle_ids | Man page Source code |
| uniprot_retrieve_proteome | Man page Source code |
| uniprot_retrieve_proteome_table | Man page Source code |
| uniprot_sample_prokaryotes | Man page Source code |
| uniprot_strata | Man page Source code |
| uniprot_weight_by_ref | Man page Source code |
| untuplify | Source code |
| use_recommended_prokaryotes | Man page Source code |
