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  "Package": "GALLO",
  "Title": "Genomic Annotation in Livestock for Positional Candidate LOci",
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  "Authors@R": "c(person(given = \"Pablo\",\nfamily = \"Fonseca\",\nrole = c(\"aut\", \"cre\"),\nemail = \"pfonseca@uoguelph.ca\"), person(\"Aroa\", \"Suarez-Vega\", email = \"asuarezv@uoguelph.ca\", role = \"aut\"),person(\"Gabriele\", \"Marras\", email = \"gmarras@semex.com\", role = \"aut\"),person(\"Angela\", \"Cánovas\", email = \"acanovas@uoguelph.ca\", role = \"aut\"))",
  "Description": "The accurate annotation of genes and Quantitative Trait\nLoci (QTLs) located within candidate markers and/or regions\n(haplotypes, windows, CNVs, etc) is a crucial step the most\ncommon genomic analyses performed in livestock, such as\nGenome-Wide Association Studies or transcriptomics. The Genomic\nAnnotation in Livestock for positional candidate LOci (GALLO)\nis an R package designed to provide an intuitive and\nstraightforward environment to annotate positional candidate\ngenes and QTLs from high-throughput genetic studies in\nlivestock. Moreover, GALLO allows the graphical visualization\nof gene and QTL annotation results, data comparison among\ndifferent grouping factors (e.g., methods, breeds, tissues,\nstatistical models, studies, etc.), and QTL enrichment in\ndifferent livestock species including cattle, pigs, sheep, and\nchicken, among others.",
  "URL": "<https://github.com/pablobio/GALLO>",
  "biocViews": "Software",
  "License": "GPL-3",
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  "Repository": "https://pablobio.r-universe.dev",
  "Date/Publication": "2021-02-26 18:59:33 UTC",
  "RemoteUrl": "https://github.com/pablobio/gallo",
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    "User": "root"
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  "Author": "Pablo Fonseca [aut, cre],\nAroa Suarez-Vega [aut],\nGabriele Marras [aut],\nAngela Cánovas [aut]",
  "Maintainer": "Pablo Fonseca <pfonseca@uoguelph.ca>",
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  "_created": "2026-07-15T04:39:51.000Z",
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    "description": "Post-Doctoral Fellow - Universidad de Leon\r\nPh.D Genetics - Genomics and Bioinformatics\r\nBiologist"
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      "date": "2020-09-01"
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    "import_gff_gtf",
    "overlapping_among_groups",
    "plot_overlapping",
    "plot_qtl_info",
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    "relationship_plot"
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      ],
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        "database",
        "QTL_type",
        "start_pos",
        "end_pos",
        "extra_info"
      ],
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      "table": true,
      "tojson": true
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      "title": "A gtf example for gene annotation",
      "object": "gtfGenes",
      "class": [
        "data.frame"
      ],
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        "start_pos",
        "end_pos",
        "width",
        "strand",
        "gene_id",
        "gene_name",
        "gene_biotype"
      ],
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      "table": true,
      "tojson": true
    },
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      "class": [
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      ],
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        "SNP.reference",
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        "CHR",
        "BP",
        "Breed",
        "Reference"
      ],
      "rows": 141,
      "table": true,
      "tojson": true
    },
    {
      "name": "QTLwindows",
      "title": "Candidate windows identified by GWAS associated with fertility traits in cattle",
      "object": "QTLwindows",
      "class": [
        "data.frame"
      ],
      "fields": [
        "First.marker.in.the.window",
        "Last.marker.in.the.window",
        "Trait",
        "CHR",
        "BP1",
        "BP2",
        "Breed",
        "Reference"
      ],
      "rows": 50,
      "table": true,
      "tojson": true
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  "_help": [
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      "page": "find_genes_qtls_around_markers",
      "title": "Search genes and QTLs around candidate regions",
      "topics": [
        "find_genes_qtls_around_markers"
      ]
    },
    {
      "page": "import_gff_gtf",
      "title": "Import .gtf and .gff files to be used during gene and QTL annotation, respectively",
      "topics": [
        "import_gff_gtf"
      ]
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      "title": "Overlapping between grouping factors",
      "topics": [
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      "title": "Plot QTLs information from the find_genes_qtls_around_markers output",
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      ]
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    {
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      "title": "Performs a QTL enrichment analysis based in a Bootstrap simulation for each QTL class",
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    },
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      "title": "Plot enrichment results for QTL enrichment analysis",
      "topics": [
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      ]
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