{
  "_id": "6a1f2458b401979e73420d51",
  "Package": "avidaR",
  "Title": "A Computational Biologist’s Toolkit To Get Data From 'avidaDB'",
  "Version": "1.2.1",
  "Authors@R": "c(person(given = \"Miguel A.\",\nfamily = \"Fortuna\",\nemail = \"fortuna@ebd.csic.es\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-8374-1941\")),\nperson(given = \"Raúl\",\nfamily = \"Ortega\",\nrole = \"cre\",\nemail = \"raul.ortega@ebd.csic.es\",\ncomment = c(ORCID = \"0000-0002-1306-5378\")))",
  "Description": "Easy-to-use tools for performing complex queries on\n'avidaDB', a semantic database that stores genomic and\ntranscriptomic data of self-replicating computer programs\n(known as digital organisms) that mutate and evolve within a\nuser-defined computational environment.",
  "License": "MIT + file LICENSE",
  "URL": "https://gitlab.com/fortunalab/avidaR",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "RoxygenNote": "7.3.1",
  "Config/testthat/edition": "3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-16 06:35:28 UTC",
    "User": "root"
  },
  "Author": "Miguel A. Fortuna [aut]\n(<https://orcid.org/0000-0002-8374-1941>), Raúl Ortega [cre]\n(<https://orcid.org/0000-0002-1306-5378>)",
  "Maintainer": "Raúl Ortega <raul.ortega@ebd.csic.es>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2024-06-22 02:39:51 UTC",
  "RemoteUrl": "https://github.com/cran/avidaR",
  "RemoteRef": "HEAD",
  "RemoteSha": "fd976f357581706fcb3512f0a41cebb323e854ba",
  "MD5sum": "b14426c095154e5527067e8664b66397",
  "_user": "cran",
  "_type": "src",
  "_file": "avidaR_1.2.1.tar.gz",
  "_fileid": "f6e92a219f8a771939bfefeefce29558ad10641db5c4ad8fb65e5333e7851810",
  "_filesize": 196713,
  "_sha256": "f6e92a219f8a771939bfefeefce29558ad10641db5c4ad8fb65e5333e7851810",
  "_created": "2026-05-16T06:35:28.000Z",
  "_published": "2026-06-02T18:43:36.679Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79146226055,
      "time": 188,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7031249681"
    },
    {
      "job": 79146226285,
      "time": 156,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7031246453"
    },
    {
      "job": 79146225279,
      "time": 190,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7031231043"
    },
    {
      "job": 79146224917,
      "time": 111,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7366790997"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/25955077771",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/avidaR",
  "_commit": {
    "id": "fd976f357581706fcb3512f0a41cebb323e854ba",
    "author": "Raúl Ortega <raul.ortega@ebd.csic.es>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.2.1\n",
    "time": 1719023991
  },
  "_maintainer": {
    "name": "Raúl Ortega",
    "email": "raul.ortega@ebd.csic.es",
    "orcid": "0000-0002-1306-5378"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "base64enc",
      "version": ">= 0.1-3",
      "role": "Imports"
    },
    {
      "package": "xml2",
      "version": ">= 1.3.2",
      "role": "Imports"
    },
    {
      "package": "httr",
      "version": ">= 1.4.2",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0.6",
      "role": "Imports"
    },
    {
      "package": "readr",
      "version": ">= 1.4.0",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "version": ">= 1.1.2",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "version": ">= 3.0.6",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "version": ">= 0.4.11",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "R6",
      "role": "Imports"
    },
    {
      "package": "curl",
      "version": ">= 5.0.2",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 257,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/avidaR"
  },
  "_devurl": "https://gitlab.com/fortunalab/avidar",
  "_searchresults": 2,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/avidaR.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://gitlab.com/fortunalab/avidar",
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2022-04-08"
    },
    {
      "version": "1.1.2",
      "date": "2022-05-30"
    },
    {
      "version": "1.1.3",
      "date": "2022-08-22"
    },
    {
      "version": "1.2.0",
      "date": "2023-09-14"
    },
    {
      "version": "1.2.1",
      "date": "2024-06-21"
    }
  ],
  "_exports": [
    "convert_org_into_seq",
    "convert_seq_into_org",
    "get_db_summary",
    "get_docker_image_from_experiment_id",
    "get_doi_from_experiment_id",
    "get_experiment_id_from_organism_id",
    "get_genome_id_from_genome_seq",
    "get_genome_id_from_logic_operation",
    "get_genome_id_from_phenotype_id",
    "get_genome_id_from_transcriptome_id",
    "get_genome_id_of_wild_type_organisms",
    "get_genome_seq_from_genome_id",
    "get_logic_operation_from_phenotype_id",
    "get_mutant_at_pos",
    "get_phenotype_id_from_genome_id",
    "get_phenotype_id_from_genome_seq",
    "get_phenotype_id_from_logic_operation",
    "get_phenotype_id_from_transcriptome_id",
    "get_tandem_id_from_genome_id",
    "get_tandem_id_from_genome_seq",
    "get_tandem_id_from_logic_operation",
    "get_tandem_id_from_phenotype_id",
    "get_tandem_seq_from_tandem_id",
    "get_transcriptome_id_from_genome_id",
    "get_transcriptome_id_from_genome_seq",
    "get_transcriptome_id_from_logic_operation",
    "get_transcriptome_id_from_phenotype_id",
    "get_transcriptome_seq_from_transcriptome_id",
    "instruction_set",
    "logic_operation",
    "plot_transcriptome",
    "triplestore_access"
  ],
  "_help": [
    {
      "page": "convert_org_into_seq",
      "title": "Converts a genome instruction sequence into a digital organism file",
      "topics": [
        "convert_org_into_seq"
      ]
    },
    {
      "page": "convert_seq_into_org",
      "title": "Converts a genome instruction sequence into a digital organism file",
      "topics": [
        "convert_seq_into_org"
      ]
    },
    {
      "page": "get_db_summary",
      "title": "Get database summary",
      "topics": [
        "get_db_summary"
      ]
    },
    {
      "page": "get_docker_image_from_experiment_id",
      "title": "Get docker image from experiment",
      "topics": [
        "get_docker_image_from_experiment_id"
      ]
    },
    {
      "page": "get_doi_from_experiment_id",
      "title": "Get doi from experiment",
      "topics": [
        "get_doi_from_experiment_id"
      ]
    },
    {
      "page": "get_experiment_id_from_organism_id",
      "title": "Get experiment from organism",
      "topics": [
        "get_experiment_id_from_organism_id"
      ]
    },
    {
      "page": "get_genome_id_from_genome_seq",
      "title": "Get genome from genome sequence",
      "topics": [
        "get_genome_id_from_genome_seq"
      ]
    },
    {
      "page": "get_genome_id_from_logic_operation",
      "title": "Get genome from logic operations",
      "topics": [
        "get_genome_id_from_logic_operation"
      ]
    },
    {
      "page": "get_genome_id_from_phenotype_id",
      "title": "Get genome from phenotype",
      "topics": [
        "get_genome_id_from_phenotype_id"
      ]
    },
    {
      "page": "get_genome_id_from_transcriptome_id",
      "title": "Get genome from transcriptome",
      "topics": [
        "get_genome_id_from_transcriptome_id"
      ]
    },
    {
      "page": "get_genome_id_of_wild_type_organisms",
      "title": "Get genomes of wild-type organisms",
      "topics": [
        "get_genome_id_of_wild_type_organisms"
      ]
    },
    {
      "page": "get_genome_seq_from_genome_id",
      "title": "Get genome sequence from genome",
      "topics": [
        "get_genome_seq_from_genome_id"
      ]
    },
    {
      "page": "get_logic_operation_from_phenotype_id",
      "title": "Get the logic operations computed by a digital organism whose genome encodes a specific phenotype",
      "topics": [
        "get_logic_operation_from_phenotype_id"
      ]
    },
    {
      "page": "get_mutant_at_pos",
      "title": "Get single-point mutants of wild-type organisms",
      "topics": [
        "get_mutant_at_pos"
      ]
    },
    {
      "page": "get_phenotype_id_from_genome_id",
      "title": "Get phenotype from genome",
      "topics": [
        "get_phenotype_id_from_genome_id"
      ]
    },
    {
      "page": "get_phenotype_id_from_genome_seq",
      "title": "Get phenotype from genome sequence",
      "topics": [
        "get_phenotype_id_from_genome_seq"
      ]
    },
    {
      "page": "get_phenotype_id_from_logic_operation",
      "title": "Get phenotype from logic operations",
      "topics": [
        "get_phenotype_id_from_logic_operation"
      ]
    },
    {
      "page": "get_phenotype_id_from_transcriptome_id",
      "title": "Get phenotype from transcriptome",
      "topics": [
        "get_phenotype_id_from_transcriptome_id"
      ]
    },
    {
      "page": "get_tandem_id_from_genome_id",
      "title": "Get tandem repeat from genome",
      "topics": [
        "get_tandem_id_from_genome_id"
      ]
    },
    {
      "page": "get_tandem_id_from_genome_seq",
      "title": "Get tandem repeat from genome sequence",
      "topics": [
        "get_tandem_id_from_genome_seq"
      ]
    },
    {
      "page": "get_tandem_id_from_logic_operation",
      "title": "Get tandem repeat from logic operations",
      "topics": [
        "get_tandem_id_from_logic_operation"
      ]
    },
    {
      "page": "get_tandem_id_from_phenotype_id",
      "title": "Get tandem repeat from phenotype",
      "topics": [
        "get_tandem_id_from_phenotype_id"
      ]
    },
    {
      "page": "get_tandem_seq_from_tandem_id",
      "title": "Get the tandem repeat sequence from tandem repeat",
      "topics": [
        "get_tandem_seq_from_tandem_id"
      ]
    },
    {
      "page": "get_transcriptome_id_from_genome_id",
      "title": "Get transcriptome from genome",
      "topics": [
        "get_transcriptome_id_from_genome_id"
      ]
    },
    {
      "page": "get_transcriptome_id_from_genome_seq",
      "title": "Get transcriptome from genome sequence",
      "topics": [
        "get_transcriptome_id_from_genome_seq"
      ]
    },
    {
      "page": "get_transcriptome_id_from_logic_operation",
      "title": "Get transcriptome from logic operations",
      "topics": [
        "get_transcriptome_id_from_logic_operation"
      ]
    },
    {
      "page": "get_transcriptome_id_from_phenotype_id",
      "title": "Get transcriptome from phenotype",
      "topics": [
        "get_transcriptome_id_from_phenotype_id"
      ]
    },
    {
      "page": "get_transcriptome_seq_from_transcriptome_id",
      "title": "Get transcriptome sequence from transcriptome",
      "topics": [
        "get_transcriptome_seq_from_transcriptome_id"
      ]
    },
    {
      "page": "instruction_set",
      "title": "Get the genetic language of Avida",
      "topics": [
        "instruction_set"
      ]
    },
    {
      "page": "logic_operation",
      "title": "Get the list of logic operations that a digital organism can compute",
      "topics": [
        "logic_operation"
      ]
    },
    {
      "page": "plot_transcriptome",
      "title": "Get a plot of the transcriptome as a chord diagram",
      "topics": [
        "plot_transcriptome"
      ]
    },
    {
      "page": "triplestore_access",
      "title": "Class to manage triplestore access options",
      "topics": [
        "triplestore_access"
      ]
    }
  ],
  "_readme": "https://github.com/cran/avidaR/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "base64enc",
    "bit",
    "bit64",
    "circlize",
    "cli",
    "clipr",
    "colorspace",
    "cpp11",
    "crayon",
    "curl",
    "dplyr",
    "generics",
    "GlobalOptions",
    "glue",
    "hms",
    "httr",
    "jsonlite",
    "lifecycle",
    "magrittr",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "RColorBrewer",
    "readr",
    "rlang",
    "shape",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "xml2"
  ],
  "_score": 1.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "avidar",
  "_universes": [
    "cran",
    "gitlab-fortunalab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.1",
      "date": "2026-05-16T06:38:14.000Z",
      "distro": "noble",
      "commit": "fd976f357581706fcb3512f0a41cebb323e854ba",
      "fileid": "b583e548bee32e253726de6833b79331a10035ffb0bfe53838c8d8bdc54eded2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25955077771"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2.1",
      "date": "2026-05-16T06:37:38.000Z",
      "distro": "noble",
      "commit": "fd976f357581706fcb3512f0a41cebb323e854ba",
      "fileid": "47f659448560b9607d4c8bb2fb24e3e5b6f80a7ec1822ffdc3949fc9b299f658",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25955077771"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.1",
      "date": "2026-06-02T18:43:18.000Z",
      "commit": "fd976f357581706fcb3512f0a41cebb323e854ba",
      "fileid": "63889a453d0f10d8ea30359cdc52df405339802795828250df01749ec75d2993",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25955077771"
    }
  ]
}