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  "Title": "Detect Annotation Releases and Repair Gene Names",
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  "Description": "Detects the species and the 'Ensembl'\n<https://www.ensembl.org> or 'GENCODE'\n<https://www.gencodegenes.org> annotation release associated\nwith a set of gene or transcript identifiers by scoring them\nagainst a bundled fingerprint of each release. Identifiers are\nthen converted to gene names using the matching release. Gene\nsymbols that spreadsheet software turned into dates or numbers\n('SEPT9' to '9-Sep') are restored to the spelling of the chosen\nrelease. Also retrieves genes by class (mitochondrial,\nsex-linked, protein-coding, ribosomal, transfer RNA, long\nnon-coding RNA), exon-union gene lengths, 'Entrez'\ncross-references, and orthologs in another species from\n'Ensembl Compara'.",
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  "Author": "Saket Choudhary [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5202-7633>)",
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    "annotate_genes",
    "AnnotateGenes",
    "build_symbol_index",
    "build_symbol_index_from_gtf",
    "BuildSymbolIndex",
    "BuildSymbolIndexFromGTF",
    "coding_genes",
    "CodingGenes",
    "compare_releases",
    "CompareReleases",
    "correct_genenames",
    "CorrectGeneNames",
    "detect_release",
    "detect_species",
    "detect_species_names",
    "DetectRelease",
    "DetectSpecies",
    "DetectSpeciesNames",
    "entrez_ids",
    "EntrezIDs",
    "fetch_mapping",
    "fetch_orthologs",
    "fetch_transcripts",
    "fetch_xrefs",
    "FetchMapping",
    "FetchOrthologs",
    "FetchTranscripts",
    "FetchXrefs",
    "gene_biotypes",
    "gene_cache",
    "gene_ids",
    "gene_lengths",
    "gene_names",
    "GeneBiotypes",
    "GeneCache",
    "geneid2name",
    "GeneID2Name",
    "GeneIDs",
    "GeneLengths",
    "GeneNames",
    "genes_by_biotype",
    "GenesByBiotype",
    "guess_scheme",
    "GuessScheme",
    "hemoglobin_genes",
    "HemoglobinGenes",
    "lncrna_genes",
    "lncRNAGenes",
    "mhc_genes",
    "MHCGenes",
    "mito_genes",
    "MitoGenes",
    "noncoding_genes",
    "NoncodingGenes",
    "ortholog_species",
    "orthologs",
    "Orthologs",
    "OrthologSpecies",
    "parse_ens",
    "ParseEns",
    "qmax_violations",
    "QmaxViolations",
    "resolve_species",
    "ResolveSpecies",
    "ribosomal_genes",
    "RibosomalGenes",
    "rrna_genes",
    "rRNAGenes",
    "sex_genes",
    "SexGenes",
    "species_table",
    "SpeciesTable",
    "stream_exon_lengths",
    "stream_gtf",
    "stream_homologies",
    "stream_transcripts",
    "stream_xrefs",
    "StreamExonLengths",
    "StreamGTF",
    "StreamHomologies",
    "StreamTranscripts",
    "StreamXrefs",
    "transcript2gene",
    "Transcript2Gene",
    "trna_genes",
    "tRNAGenes"
  ],
  "_help": [
    {
      "page": "aggregate_transcripts",
      "title": "Sum transcript-level counts to gene level",
      "topics": [
        "AggregateTranscripts",
        "aggregate_transcripts"
      ]
    },
    {
      "page": "annotate_genes",
      "title": "Everything the annotation knows about a set of genes",
      "topics": [
        "AnnotateGenes",
        "annotate_genes"
      ]
    },
    {
      "page": "build_symbol_index",
      "title": "Build a compact species/release gene-symbol index from GTF mappings",
      "topics": [
        "BuildSymbolIndex",
        "build_symbol_index"
      ]
    },
    {
      "page": "build_symbol_index_from_gtf",
      "title": "Fetch GTF mappings and build a symbol index",
      "topics": [
        "BuildSymbolIndexFromGTF",
        "build_symbol_index_from_gtf"
      ]
    },
    {
      "page": "coding_genes",
      "title": "Protein-coding genes",
      "topics": [
        "CodingGenes",
        "coding_genes"
      ]
    },
    {
      "page": "compare_releases",
      "title": "Compare two releases of one annotation",
      "topics": [
        "CompareReleases",
        "compare_releases"
      ]
    },
    {
      "page": "correct_genenames",
      "title": "Repair gene symbols a spreadsheet has converted to dates or numbers",
      "topics": [
        "CorrectGeneNames",
        "correct_genenames"
      ]
    },
    {
      "page": "detect_release",
      "title": "Which Ensembl release a set of identifiers came from",
      "topics": [
        "DetectRelease",
        "detect_release"
      ]
    },
    {
      "page": "detect_species",
      "title": "Which species a set of identifiers belongs to",
      "topics": [
        "DetectSpecies",
        "detect_species"
      ]
    },
    {
      "page": "detect_species_names",
      "title": "Detect species from gene symbols",
      "topics": [
        "DetectSpeciesNames",
        "detect_species_names"
      ]
    },
    {
      "page": "entrez_ids",
      "title": "NCBI Entrez identifiers for a set of genes",
      "topics": [
        "EntrezIDs",
        "entrez_ids"
      ]
    },
    {
      "page": "fetch_mapping",
      "title": "Mapping table for one species and Ensembl release",
      "topics": [
        "FetchMapping",
        "fetch_mapping"
      ]
    },
    {
      "page": "fetch_orthologs",
      "title": "Ortholog table for one species pair and Ensembl release",
      "topics": [
        "FetchOrthologs",
        "fetch_orthologs"
      ]
    },
    {
      "page": "fetch_transcripts",
      "title": "Transcript-to-gene table for one species and release",
      "topics": [
        "FetchTranscripts",
        "fetch_transcripts"
      ]
    },
    {
      "page": "fetch_xrefs",
      "title": "Ensembl gene identifiers and their cross-references, cached",
      "topics": [
        "FetchXrefs",
        "fetch_xrefs"
      ]
    },
    {
      "page": "gene_biotypes",
      "title": "What biotypes an annotation contains",
      "topics": [
        "GeneBiotypes",
        "gene_biotypes"
      ]
    },
    {
      "page": "gene_cache",
      "title": "Inspect or clear the download cache",
      "topics": [
        "GeneCache",
        "gene_cache"
      ]
    },
    {
      "page": "gene_ids",
      "title": "Gene identifiers for gene names or Entrez identifiers",
      "topics": [
        "GeneIDs",
        "gene_ids"
      ]
    },
    {
      "page": "gene_lengths",
      "title": "Exon-union gene lengths for one species and release",
      "topics": [
        "GeneLengths",
        "gene_lengths"
      ]
    },
    {
      "page": "gene_names",
      "title": "Convert gene identifiers to gene names",
      "topics": [
        "GeneNames",
        "gene_names"
      ]
    },
    {
      "page": "geneid2name",
      "title": "Convert gene identifiers to gene names, detecting species and release",
      "topics": [
        "GeneID2Name",
        "geneid2name"
      ]
    },
    {
      "page": "genes_by_biotype",
      "title": "Genes of a given biotype, or class of biotypes",
      "topics": [
        "GenesByBiotype",
        "genes_by_biotype"
      ]
    },
    {
      "page": "guess_scheme",
      "title": "Which identifier scheme a vector of IDs uses",
      "topics": [
        "GuessScheme",
        "guess_scheme"
      ]
    },
    {
      "page": "hemoglobin_genes",
      "title": "Hemoglobin subunit genes",
      "topics": [
        "HemoglobinGenes",
        "hemoglobin_genes"
      ]
    },
    {
      "page": "lncrna_genes",
      "title": "Long non-coding RNA genes",
      "topics": [
        "lncRNAGenes",
        "lncrna_genes"
      ]
    },
    {
      "page": "mhc_genes",
      "title": "Major histocompatibility complex genes",
      "topics": [
        "MHCGenes",
        "mhc_genes"
      ]
    },
    {
      "page": "mito_genes",
      "title": "Mitochondrial genes",
      "topics": [
        "MitoGenes",
        "mito_genes"
      ]
    },
    {
      "page": "noncoding_genes",
      "title": "Non-coding RNA genes",
      "topics": [
        "NoncodingGenes",
        "noncoding_genes"
      ]
    },
    {
      "page": "ortholog_species",
      "title": "Species Compara publishes homologies for",
      "topics": [
        "OrthologSpecies",
        "ortholog_species"
      ]
    },
    {
      "page": "orthologs",
      "title": "Find orthologs of gene identifiers in another species",
      "topics": [
        "Orthologs",
        "orthologs"
      ]
    },
    {
      "page": "parse_ens",
      "title": "Parse Ensembl identifiers into their parts",
      "topics": [
        "ParseEns",
        "parse_ens"
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    },
    {
      "page": "qmax_violations",
      "title": "Where the index violates its own ordering invariant",
      "topics": [
        "QmaxViolations",
        "qmax_violations"
      ]
    },
    {
      "page": "resolve_species",
      "title": "Resolve a species name",
      "topics": [
        "ResolveSpecies",
        "resolve_species"
      ]
    },
    {
      "page": "ribosomal_genes",
      "title": "Ribosomal genes",
      "topics": [
        "RibosomalGenes",
        "ribosomal_genes"
      ]
    },
    {
      "page": "rrna_genes",
      "title": "Ribosomal RNA genes",
      "topics": [
        "rRNAGenes",
        "rrna_genes"
      ]
    },
    {
      "page": "sex_genes",
      "title": "Sex-chromosome genes",
      "topics": [
        "SexGenes",
        "sex_genes"
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    },
    {
      "page": "species_table",
      "title": "Species the index covers, with their common names",
      "topics": [
        "SpeciesTable",
        "species_table"
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    },
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      "title": "Exon-union lengths from a GTF, streamed without writing it to disk",
      "topics": [
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        "stream_exon_lengths"
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        "stream_gtf"
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        "transcript2gene"
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