aggregate_transcripts   Sum transcript-level counts to gene level
annotate_genes          Everything the annotation knows about a set of
                        genes
build_symbol_index      Build a compact species/release gene-symbol
                        index from GTF mappings
build_symbol_index_from_gtf
                        Fetch GTF mappings and build a symbol index
coding_genes            Protein-coding genes
compare_releases        Compare two releases of one annotation
correct_genenames       Repair gene symbols a spreadsheet has converted
                        to dates or numbers
detect_release          Which Ensembl release a set of identifiers came
                        from
detect_species          Which species a set of identifiers belongs to
detect_species_names    Detect species from gene symbols
entrez_ids              NCBI Entrez identifiers for a set of genes
fetch_mapping           Mapping table for one species and Ensembl
                        release
fetch_orthologs         Ortholog table for one species pair and Ensembl
                        release
fetch_transcripts       Transcript-to-gene table for one species and
                        release
fetch_xrefs             Ensembl gene identifiers and their
                        cross-references, cached
gene_biotypes           What biotypes an annotation contains
gene_cache              Inspect or clear the download cache
gene_ids                Gene identifiers for gene names or Entrez
                        identifiers
gene_lengths            Exon-union gene lengths for one species and
                        release
gene_names              Convert gene identifiers to gene names
geneid2name             Convert gene identifiers to gene names,
                        detecting species and release
genes_by_biotype        Genes of a given biotype, or class of biotypes
guess_scheme            Which identifier scheme a vector of IDs uses
hemoglobin_genes        Hemoglobin subunit genes
lncrna_genes            Long non-coding RNA genes
mhc_genes               Major histocompatibility complex genes
mito_genes              Mitochondrial genes
noncoding_genes         Non-coding RNA genes
ortholog_species        Species Compara publishes homologies for
orthologs               Find orthologs of gene identifiers in another
                        species
parse_ens               Parse Ensembl identifiers into their parts
qmax_violations         Where the index violates its own ordering
                        invariant
resolve_species         Resolve a species name
ribosomal_genes         Ribosomal genes
rrna_genes              Ribosomal RNA genes
sex_genes               Sex-chromosome genes
species_table           Species the index covers, with their common
                        names
stream_exon_lengths     Exon-union lengths from a GTF, streamed without
                        writing it to disk
stream_gtf              Pull gene records out of a GTF without ever
                        writing it to disk
stream_homologies       Stream one species' orthologs against one other
                        species
stream_transcripts      Transcript-to-gene records from a GTF, streamed
                        without writing it to disk
stream_xrefs            Stream one cross-reference TSV, keeping the
                        gene-level pairs
transcript2gene         Map transcript identifiers to their genes
trna_genes              Transfer RNA genes
