| add_organelle_proteins | Add organelle ID lists for each proteome |
| add_proteome_stats | Add proteome stats for each proteome |
| add_taxa | Add an id to a representative list |
| arabidopsis | Arabidopsis thaliana vignette data |
| arabidopsis_strata | An Arabidopsis thaliana based Strata object |
| atree | A simple, bifurcating tree for use in util examples |
| children | Get the immediate children of a node |
| classify_by_adjusted_pvalue | Infer homology inference based on an adjusted p-value... |
| classify_by_evalue | Infer homology inference based on a hard e-value threshold |
| classify_by_pvalue | Infer homology inference based on a hard p-value threshold |
| clean_phyid | Convert node/tip name to id, check size |
| constrict | Find the focal sequences that are not represented in the... |
| CountMatrix | Initialize a CountMatrix object |
| data_tree_to_result_tree | Convert sequence tree to result tree |
| descendent_nodes | Get all nodes (leafs and ancestors) descending from, and... |
| descendents | Get all leafs descending from a set of ids |
| diverse_subtree | Get a diverse subset of species from tree |
| edgelist_to_phylo | Make a phylo object from an edgelist |
| extract_uniprot_id_from_fasta | Parse a UniProt ID from a FASTA file |
| find_revenants | Find genes that with matches that skip strata |
| get_besthit | Get the "besthit" table for a given species |
| get_max_hit | Get the maximum hit |
| get_mrca_names | Get an ordered factor mapping MRCA taxon IDs (as vector... |
| get_phylostrata_map | Get a phylostrata map from a Strata object |
| get_root | Get the root of a tree |
| has_header | Ensure the first line of a file has contains all of the... |
| homolog_tree_to_phylostrata | Convert a homolog tree to a phylostrata table |
| is_root | Vectorized tree root finder |
| is_valid_strata | Assert a Strata object is valid, die on failure |
| leafs | Get leaf indices |
| lineage | Find the ancestors of a node |
| lineages_to_phylo | Make a tree from the union of lineages |
| lineage_to_ancestor_tree | Make a tree of ancestors from a lineage |
| load_hittable | Load a table of scored matches |
| make_blast_database | Build a blast database for one species |
| make_diamond_database | Build a diamond database for one species author urmi |
| make_jump_matrix | Get comparisons of inferences across scoring systems |
| make_matrix_from_two_strata | Make a count matrix from two strata |
| make_significance_matrices | Get comparisons of inferences across scoring systems |
| make_tree_relative_to | Organize the tips with the focal_id on tip |
| map_ids | Map indices from a to b based off tip labels |
| map_node_label | Map nodes names from a to b |
| merge_besthits | Build a single data.frame with an MRCA column from stratified... |
| merge_phylo | Merge fully named subtrees according to a reference tree |
| ncbi_ancestors | Get the lineage of a given species |
| ncbi_aunts | Get all ancestral sisters of a taxon |
| ncbi_cousins | Get the species level cousins of a taxid |
| ncbi_tree | Build a phylogenetic tree from a list of NCBI taxon IDs |
| nleafs | Get the number of leafs |
| nodes | Get node indices |
| normalize_matrix_by_col | Normalize a matrix such that columns sum to 1 |
| normalize_matrix_by_row | Normalize a matrix such that rows sum to 1 |
| organelle_table | Build a table of organelle count statistics |
| parent | Vectorized node parent getter |
| partial_id_to_name | Convert vector of mixed IDs and names to a vector of names |
| phylostratr | phylostratr: Phylostratigraphy execution and analysis |
| plot.CountMatrix | Plot a CountMatrix object |
| plot_heatmaps | Plots for the hit distribution of all genes |
| plot_phyloheatmap | Build a phylostratigraphic heatmap |
| plot_proteome_lengths | Plot the ordered lengths of all proteins in all proteomes |
| plot_proteome_stats | Plot summary statistics for all proteomes |
| plot.Strata | Plot a Strata object |
| print.Strata | Strata print generic function |
| proteome_report_table | Generate a summary table of proteome stats |
| proteome_stats_table | Build a table of proteome statistics |
| prune | Remove the specified indices, and their descendents, from the... |
| prune_phylostrata | Given a strata table, remove given strata |
| query_sparql | Execute a SPARQL query |
| read_blast | Read a blast result of the form expected by phylostratr |
| rename_species | Rename a species in a Strata object |
| replace_branch | Replace a branch on a Strata |
| result_tree_to_homolog_tree | Convert tree of p-values to a homolog tree |
| result_tree_to_pvalue_tree | Convert tree of raw results to a p-value tree |
| run_blastp | BLAST query protein FASTA file against a subject species |
| run_diamond_blastp | BLAST query protein FASTA file against a subject species... |
| run_hmmscan | Find domains in a protein file |
| saccharomyces | A custom Strata object for the Saccharomyces genus |
| set_node_names | If nodes are not named, give them default names |
| sisters | Get the sisters of a node |
| sister_trees | Get list of sister trees for a given node |
| sort_strata | Sort strata relative to focal species |
| species_to_species_tree | Get a species tree tracing back to origin for the focal... |
| species_tree_to_data_tree | Acquire the protein sequence of each species |
| standardize_strata | Standardize two or more phylostrata tables |
| Strata | Initialize a Strata object |
| strata_apply | Apply f to each outgroup branch ascending node id |
| strata_besthits | Load each blast result and filter out the best hit against... |
| strata_blast | Blast strata |
| strata_convert | Convert strata data, tip, and node names to and from NCBI... |
| strata_diamond | author urmi Blast strata using diamond blastp |
| strata_from_blast_dir | Build a Strata object from a directory of BLAST results |
| strata_from_taxids | Make a Strata object from a list of taxon ids |
| strata_map | Apply f to each outgroup branch ascending node id, returning... |
| strata_uniprot_pfam_map | Retrieve uniprot to pfam maps for all taxa |
| stratify | Get the phylostratum of each query gene |
| subset_fasta | Select ids from a FASTA file, creating a new file |
| subtree | Select a subset of nodes from a tree |
| t.CountMatrix | Transpose a CountMatrix |
| thin_fasta | Select n entries from a FASTA file, creating a new file |
| tree2edgelist | Convert a tree to an edge list |
| tree_names | Get the names of all leafs and nodes in a tree |
| tree_size | Get the number of species and ancestors in the tree |
| uniprot_add_idmap | Extract an ID map from uniprot fasta files |
| uniprot_downstream_ids | Get the uniprot ids downstream of a node |
| uniprot_fill_strata | Download sequence data for each species in a UniProt-based... |
| uniprot_map2pfam | Map UniProt IDs for an organism to PFAM IDs |
| uniprot_organelle_ids | Get the uniprot ids for organelle proteins of a given taxid |
| uniprot_retrieve_proteome | Retrieve UniProt proteome |
| uniprot_retrieve_proteome_table | Retrieve UniProt proteome table |
| uniprot_sample_prokaryotes | Randomly sample prokaryotic representatives |
| uniprot_strata | Given a focal taxid, build a UniProt-based Strata object |
| uniprot_weight_by_ref | Make reference-species preferring weight vector for... |
| use_recommended_prokaryotes | Use the prokaryotic species that I use |
