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  "Package": "OmaDB",
  "Title": "R wrapper for the OMA REST API",
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  "Author": "Klara Kaleb",
  "Maintainer": "Klara Kaleb <klara.kaleb18@ic.ac.uk>, Adrian Altenhoff\n<adrian.altenhoff@inf.ethz.ch>",
  "Description": "A package for the orthology prediction data download from\nOMA database.",
  "URL": "https://github.com/DessimozLab/OmaDB",
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    "getAnnotation",
    "getAttribute",
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    "getProtein",
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    "getTopGO",
    "getTree",
    "getVersion",
    "getXref",
    "mapSequence",
    "resolveURL",
    "searchProtein",
    "setAPI"
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      "name": "group",
      "title": "An example OMA group object.",
      "object": "group",
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        "list"
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      "table": false,
      "tojson": true
    },
    {
      "name": "hog",
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      "object": "hog",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "orthologs",
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      "class": [
        "data.frame"
      ],
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        "entry_nr",
        "entry_url",
        "omaid",
        "canonicalid",
        "sequence_md5",
        "oma_group",
        "oma_hog_id",
        "chromosome",
        "locus.start",
        "locus.end",
        "locus.strand",
        "is_main_isoform",
        "rel_type",
        "distance",
        "score"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "pairs",
      "title": "An example genome alignment object.",
      "object": "pairs",
      "class": [
        "data.frame"
      ],
      "fields": [
        "entry_1.entry_nr",
        "entry_1.entry_url",
        "entry_1.omaid",
        "entry_1.canonicalid",
        "entry_1.sequence_md5",
        "entry_1.oma_group",
        "entry_1.oma_hog_id",
        "entry_1.chromosome",
        "entry_1.locus.start",
        "entry_1.locus.end",
        "entry_1.locus.strand",
        "entry_1.is_main_isoform",
        "entry_2.entry_nr",
        "entry_2.entry_url",
        "entry_2.omaid",
        "entry_2.canonicalid",
        "entry_2.sequence_md5",
        "entry_2.oma_group",
        "entry_2.oma_hog_id",
        "entry_2.chromosome",
        "entry_2.locus.start",
        "entry_2.locus.end",
        "entry_2.locus.strand",
        "entry_2.is_main_isoform",
        "rel_type",
        "distance",
        "score"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "protein",
      "title": "An example protein object.",
      "object": "protein",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sequence_annotation",
      "title": "An example dataframe containing GO annotations identified from a given sequence.",
      "object": "sequence_annotation",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Qualifier",
        "GO_ID",
        "With",
        "Evidence",
        "Date",
        "DB_Object_Type",
        "DB_Object_Name",
        "Aspect",
        "Assigned_By",
        "GO_name",
        "DB",
        "DB.Reference",
        "Synonym"
      ],
      "rows": 6,
      "table": true,
      "tojson": true
    },
    {
      "name": "sequence_map",
      "title": "An example dataframe containing proteins identified from a given sequence.",
      "object": "sequence_map",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "taxonomy",
      "title": "An example newick format taxonomy object.",
      "object": "taxonomy",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "xref",
      "title": "An example xref object.",
      "object": "xref",
      "class": [
        "data.frame"
      ],
      "fields": [
        "xref",
        "source",
        "entry_nr",
        "omaid",
        "genome.code",
        "genome.taxon_id",
        "genome.species",
        "genome.genome_url"
      ],
      "rows": 2257,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "OmaDB-package",
      "title": "OmaDB: A package for the orthology prediction data download from OMA database.",
      "topics": [
        "OmaDB-package",
        "OmaDB"
      ]
    },
    {
      "page": "cash-.omadb_obj",
      "title": "Resolve URLs automatically when accessed",
      "topics": [
        "$.omadb_obj"
      ]
    },
    {
      "page": "annotateSequence",
      "title": "Map GO annotation to a sequence that is not available in the OMA Browser",
      "topics": [
        "annotateSequence"
      ]
    },
    {
      "page": "formatTopGO",
      "title": "Format the GO annotations data",
      "topics": [
        "formatTopGO"
      ]
    },
    {
      "page": "getAttribute",
      "title": "Get the value for the Object Attribute",
      "topics": [
        "getAttribute"
      ]
    },
    {
      "page": "getGenome",
      "title": "Retrieve a genome from the OMA Browser database",
      "topics": [
        "getGenome"
      ]
    },
    {
      "page": "getGenomePairs",
      "title": "Retrieves the pairwise relations among two genomes",
      "topics": [
        "getGenomePairs"
      ]
    },
    {
      "page": "getHOG",
      "title": "Retrieve a HOG from the OMA Browser",
      "topics": [
        "getHOG"
      ]
    },
    {
      "page": "getLocus",
      "title": "Get loci for a given list of proteins",
      "topics": [
        "getLocus"
      ]
    },
    {
      "page": "getObjectAttributes",
      "title": "Get the Object Attributes",
      "topics": [
        "getObjectAttributes"
      ]
    },
    {
      "page": "getOMAGroup",
      "title": "Retrieve an OMA Group from the OMA Browser",
      "topics": [
        "getOMAGroup"
      ]
    },
    {
      "page": "getProtein",
      "title": "Retrieve a protein from the OMA Browser",
      "topics": [
        "getProtein"
      ]
    },
    {
      "page": "getTaxonomy",
      "title": "Get the Taxonomic tree function",
      "topics": [
        "getTaxonomy"
      ]
    },
    {
      "page": "getTopGO",
      "title": "Get the topGO Object function",
      "topics": [
        "getTopGO"
      ]
    },
    {
      "page": "getTree",
      "title": "Get the Tree Object",
      "topics": [
        "getTree"
      ]
    },
    {
      "page": "getVersion",
      "title": "Get the API and database version function",
      "topics": [
        "getVersion"
      ]
    },
    {
      "page": "group",
      "title": "An example OMA group object.",
      "topics": [
        "group"
      ]
    },
    {
      "page": "hog",
      "title": "An example HOG object.",
      "topics": [
        "hog"
      ]
    },
    {
      "page": "mapSequence",
      "title": "Map the Protein Sequence Function",
      "topics": [
        "mapSequence"
      ]
    },
    {
      "page": "orthologs",
      "title": "An example orthologs object.",
      "topics": [
        "orthologs"
      ]
    },
    {
      "page": "pairs",
      "title": "An example genome alignment object.",
      "topics": [
        "pairs"
      ]
    },
    {
      "page": "protein",
      "title": "An example protein object.",
      "topics": [
        "protein"
      ]
    },
    {
      "page": "resolveURL",
      "title": "Load data for a given url from the OMA Browser API.",
      "topics": [
        "resolveURL"
      ]
    },
    {
      "page": "searchProtein",
      "title": "Get the CrossReferences in the OMA database for a pattern",
      "topics": [
        "searchProtein"
      ]
    },
    {
      "page": "sequence_annotation",
      "title": "An example dataframe containing GO annotations identified from a given sequence.",
      "topics": [
        "sequence_annotation"
      ]
    },
    {
      "page": "sequence_map",
      "title": "An example dataframe containing proteins identified from a given sequence.",
      "topics": [
        "sequence_map"
      ]
    },
    {
      "page": "setAPI",
      "title": "Set the url to the OMA Browser API",
      "topics": [
        "setAPI"
      ]
    },
    {
      "page": "taxonomy",
      "title": "An example newick format taxonomy object.",
      "topics": [
        "taxonomy"
      ]
    },
    {
      "page": "xref",
      "title": "An example xref object.",
      "topics": [
        "xref"
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      "headings": [
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      "headings": [],
      "created": "2017-10-12 19:26:48",
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