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  "Package": "annotationTools",
  "Version": "1.86.0",
  "Date": "2020-03-27",
  "Title": "Annotate microarrays and perform cross-species gene expression\nanalyses using flat file databases",
  "Author": "Alexandre Kuhn <alexandre.m.kuhn@gmail.com>",
  "Maintainer": "Alexandre Kuhn <alexandre.m.kuhn@gmail.com>",
  "Description": "Functions to annotate microarrays, find orthologs, and\nintegrate heterogeneous gene expression profiles using\nannotation and other molecular biology information available as\nflat file database (plain text files).",
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      "file": "orthologs_example.RData",
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        "Species.Scientific.Name",
        "Annotation.Date",
        "Sequence.Type",
        "Sequence.Source",
        "Transcript.ID.Array.Design.",
        "Target.Description",
        "Representative.Public.ID",
        "Archival.UniGene.Cluster",
        "UniGene.ID",
        "Genome.Version",
        "Alignments",
        "Gene.Title",
        "Gene.Symbol",
        "Chromosomal.Location",
        "Unigene.Cluster.Type",
        "Ensembl",
        "Entrez.Gene",
        "SwissProt",
        "EC",
        "OMIM",
        "RefSeq.Protein.ID",
        "RefSeq.Transcript.ID",
        "FlyBase",
        "AGI",
        "WormBase",
        "MGI.Name",
        "RGD.Name",
        "SGD.accession.number",
        "Gene.Ontology.Biological.Process",
        "Gene.Ontology.Cellular.Component",
        "Gene.Ontology.Molecular.Function",
        "Pathway",
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        "QTL",
        "Annotation.Description",
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        "Transcript.Assignments",
        "Annotation.Notes"
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      "title": "ortho",
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      "file": "orthologs_example.RData",
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        "gid1",
        "gid2",
        "ps2"
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      "tojson": true
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      "name": "table_human",
      "title": "table\\_human",
      "object": "orthologs_example",
      "file": "orthologs_example.RData",
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        "P.Value.caudate",
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        "Probe.Set.ID",
        "UniGene.ID",
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        "Gene.Ontology.Biological.Process",
        "Gene.Ontology.Cellular.Component",
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        "t",
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        "Probe.Set.ID",
        "Title",
        "Gene.Symbol"
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      "page": "compactList",
      "title": "Concatenate list elements",
      "topics": [
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    {
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      "title": "Example gene_orthologs file",
      "topics": [
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      "title": "General annotation function",
      "topics": [
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    {
      "page": "getGENEID",
      "title": "Find gene IDs",
      "topics": [
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    {
      "page": "getGENEONTOLOGY",
      "title": "Find Gene Ontology (GO) annotation",
      "topics": [
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    {
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      "title": "Find gene symbols",
      "topics": [
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      "page": "getGENETITLE",
      "title": "Find gene titles",
      "topics": [
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      "topics": [
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      "title": "Find probe set IDs",
      "topics": [
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      "title": "Example Affymetrix annotation file",
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      "title": "Example HomoloGene file",
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      "title": "Turn list into character vector",
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      "title": "Example Affymetrix annotation file",
      "topics": [
        "Mouse430_2_annot_part"
      ]
    },
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      "title": "ortho",
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      "title": "Find orthologous/homologous probe sets across two different Affymetrix microarray formats using a table of orthologs",
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