{
  "_id": "6a4989246d67900babdf9a59",
  "Package": "agvgd",
  "Type": "Package",
  "Title": "An R Implementation of the 'Align-GVGD' Method",
  "Version": "0.1.2",
  "Authors@R": "c(\nperson(given = \"Ramiro\", family = \"Magno\",\nemail = \"ramiro.magno@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5226-3441\")),\nperson(given = \"Isabel\", family = \"Duarte\",\nemail = \"iduarte.scientist@gmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-0060-2936\")),\nperson(given = \"Ana-Teresa\", family = \"Maia\",\nemail = \"maia.anateresa@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-0454-9207\")),\nperson(\"CINTESIS\",\nrole = c(\"cph\", \"fnd\"))\n)",
  "Description": "'Align-GVGD' ('A-GVGD') is a method to predict the impact\nof 'missense' substitutions based on the properties of amino\nacid side chains and protein multiple sequence alignments\n<doi:10.1136/jmg.2005.033878>. 'A-GVGD' is an extension of the\noriginal 'Grantham' distance to multiple sequence alignments.\nThis package provides an alternative R implementation to the\nweb version found on <http://agvgd.hci.utah.edu/>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.3",
  "Config/testthat/edition": "3",
  "URL": "https://maialab.org/agvgd/, https://github.com/maialab/agvgd",
  "BugReports": "https://github.com/maialab/agvgd/issues",
  "Remotes": [
    "maialab/protean"
  ],
  "Config/pak/sysreqs": "libicu-dev zlib1g-dev",
  "Repository": "https://patterninstitute.r-universe.dev",
  "Date/Publication": "2023-12-16 15:22:43 UTC",
  "RemoteUrl": "https://github.com/maialab/agvgd",
  "RemoteRef": "HEAD",
  "RemoteSha": "4e746e319e67d53f4722794148e6b03299e4ad72",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-22 07:57:37 UTC",
    "User": "root"
  },
  "Author": "Ramiro Magno [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5226-3441>),\nIsabel Duarte [aut] (ORCID: <https://orcid.org/0000-0003-0060-2936>),\nAna-Teresa Maia [aut] (ORCID: <https://orcid.org/0000-0002-0454-9207>),\nCINTESIS [cph, fnd]",
  "Maintainer": "Ramiro Magno <ramiro.magno@gmail.com>",
  "_user": "patterninstitute",
  "_type": "src",
  "_file": "agvgd_0.1.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/abde24a21cf0b38410d5b60d835d40e56bfa090ed26f341b358e7a7c2e205fc6",
  "_filesize": 1746067,
  "_sha256": "abde24a21cf0b38410d5b60d835d40e56bfa090ed26f341b358e7a7c2e205fc6",
  "_expires": "2026-10-12T22:28:50.000Z",
  "_created": "2026-06-22T07:57:37.000Z",
  "_published": "2026-07-04T22:28:52.489Z",
  "_jobs": [
    {
      "job": 85172205728,
      "time": 149,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7786360985"
    },
    {
      "job": 85172205718,
      "time": 154,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7786362687"
    },
    {
      "job": 85172205749,
      "time": 97,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7786343122"
    },
    {
      "job": 85172205604,
      "time": 104,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7786345901"
    },
    {
      "job": 82663819944,
      "time": 238,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7786309965"
    },
    {
      "job": 85172205747,
      "time": 121,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7786351581"
    },
    {
      "job": 85172205631,
      "time": 94,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7786342974"
    },
    {
      "job": 85172205730,
      "time": 87,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7786340054"
    },
    {
      "job": 85172205625,
      "time": 100,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7786344581"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/patterninstitute/actions/runs/27937841642",
  "_status": "success",
  "_upstream": "https://github.com/maialab/agvgd",
  "_commit": {
    "id": "4e746e319e67d53f4722794148e6b03299e4ad72",
    "author": "Ramiro Magno <rmagno@pattern.institute>",
    "committer": "Ramiro Magno <rmagno@pattern.institute>",
    "message": "Update article `correia_magno2022`\n\n- Changed dependency on tidyverse to dplyr\n- Replace magrittr' pipe by R base pipe\n",
    "time": 1702740163
  },
  "_maintainer": {
    "name": "Ramiro Magno",
    "email": "ramiro.magno@gmail.com",
    "login": "ramiromagno",
    "description": "Lead Data Scientist",
    "uuid": 19862384,
    "orcid": "0000-0001-5226-3441"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "crayon",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "grantham",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "seqinr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "vctrs",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "protean",
      "version": ">= 0.1.1",
      "role": "Enhances"
    }
  ],
  "_owner": "maialab",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "ramiromagno",
      "count": 70,
      "uuid": 19862384
    },
    {
      "user": "iduarte",
      "count": 1,
      "uuid": 21247816
    }
  ],
  "_userbio": {
    "uuid": 115077578,
    "type": "organization",
    "name": "Pattern Institute",
    "followers": 8,
    "description": "Non-profit research organization"
  },
  "_downloads": {
    "count": 318,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/agvgd"
  },
  "_devurl": "https://github.com/maialab/agvgd",
  "_pkgdown": "https://maialab.org/agvgd/",
  "_searchresults": 6,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/agvgd.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",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/maialab/agvgd",
  "_realowner": "maialab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2022-01-17"
    },
    {
      "version": "0.1.1",
      "date": "2022-02-03"
    },
    {
      "version": "0.1.2",
      "date": "2022-09-10"
    }
  ],
  "_exports": [
    "%>%",
    "agvgd",
    "alignment_file",
    "amino_acids",
    "cpv_ranges",
    "dev",
    "gd",
    "gv",
    "poi_to_res",
    "profile_to_alignment",
    "read_agvgdweb_results",
    "read_alignment",
    "read_substitutions",
    "res_to_poi",
    "write_alignment",
    "write_substitutions"
  ],
  "_help": [
    {
      "page": "agvgd",
      "title": "Align-GVGD (A-GVGD)",
      "topics": [
        "agvgd"
      ]
    },
    {
      "page": "alignment_file",
      "title": "Pre-bundled alignments",
      "topics": [
        "alignment_file"
      ]
    },
    {
      "page": "amino_acids",
      "title": "The 20 standard amino acids",
      "topics": [
        "amino_acids"
      ]
    },
    {
      "page": "cpv_ranges",
      "title": "Determine CPV ranges",
      "topics": [
        "cpv_ranges"
      ]
    },
    {
      "page": "dev",
      "title": "Deviation function",
      "topics": [
        "dev"
      ]
    },
    {
      "page": "gd",
      "title": "Grantham deviation",
      "topics": [
        "gd"
      ]
    },
    {
      "page": "gv",
      "title": "Grantham variation",
      "topics": [
        "gv"
      ]
    },
    {
      "page": "poi_to_res",
      "title": "Convert an alignment position to residue position",
      "topics": [
        "poi_to_res"
      ]
    },
    {
      "page": "profile_to_alignment",
      "title": "Converts a sequence profile to an alignment",
      "topics": [
        "profile_to_alignment"
      ]
    },
    {
      "page": "read_alignment",
      "title": "Read a protein sequence multiple alignment",
      "topics": [
        "read_alignment"
      ]
    },
    {
      "page": "read_substitutions",
      "title": "Read a file with amino acid substitutions",
      "topics": [
        "read_substitutions"
      ]
    },
    {
      "page": "res_to_poi",
      "title": "Convert a residue position to an alignment position",
      "topics": [
        "res_to_poi"
      ]
    },
    {
      "page": "write_alignment",
      "title": "Export an alignment to FASTA",
      "topics": [
        "write_alignment"
      ]
    },
    {
      "page": "write_substitutions",
      "title": "Generate and export a list of substitutions",
      "topics": [
        "write_substitutions"
      ]
    }
  ],
  "_pkglogo": "https://github.com/maialab/agvgd/raw/HEAD/man/figures/logo.svg",
  "_readme": "https://github.com/maialab/agvgd/raw/HEAD/README.md",
  "_rundeps": [
    "ade4",
    "cli",
    "cpp11",
    "crayon",
    "dplyr",
    "generics",
    "glue",
    "grantham",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "nlme",
    "pillar",
    "pixmap",
    "pkgconfig",
    "purrr",
    "R6",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "segmented",
    "seqinr",
    "sp",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_score": 3.1760912590556813,
  "_indexed": false,
  "_nocasepkg": "agvgd",
  "_universes": [
    "patterninstitute"
  ],
  "_indexurl": "https://maialab.r-universe.dev/agvgd",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-06-22T08:00:01.000Z",
      "distro": "noble",
      "commit": "4e746e319e67d53f4722794148e6b03299e4ad72",
      "fileid": "https://r2.ropensci.org/d89895a62056bcce50ef566dc03525b637778c0aa657617f35a749acda4ac5fe",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/patterninstitute/actions/runs/27937841642"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-06-22T08:00:07.000Z",
      "distro": "noble",
      "commit": "4e746e319e67d53f4722794148e6b03299e4ad72",
      "fileid": "https://r2.ropensci.org/19d82dca5fb5a3385c3c8eb65423a99defffbbb852fe12dcccd2a0d3203c35f5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/patterninstitute/actions/runs/27937841642"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-06-22T07:59:15.000Z",
      "commit": "4e746e319e67d53f4722794148e6b03299e4ad72",
      "fileid": "https://r2.ropensci.org/0de0ffc721c5a933491f816c0b9bbfc03634a60fba377458d434c951e4ef830d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/patterninstitute/actions/runs/27937841642"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-06-22T07:59:19.000Z",
      "commit": "4e746e319e67d53f4722794148e6b03299e4ad72",
      "fileid": "https://r2.ropensci.org/6fe3be6f0410d7ca1bf88ae509c6b9f3d658b66253b97c5faa305d364e0ea094",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/patterninstitute/actions/runs/27937841642"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.2",
      "date": "2026-06-22T07:59:55.000Z",
      "commit": "4e746e319e67d53f4722794148e6b03299e4ad72",
      "fileid": "https://r2.ropensci.org/5f06c16b1afd553508f947d33257af151ab03a377b8b8e29b090df7bb8647600",
      "status": "success",
      "buildurl": "https://github.com/r-universe/patterninstitute/actions/runs/27937841642"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-06-22T07:59:03.000Z",
      "commit": "4e746e319e67d53f4722794148e6b03299e4ad72",
      "fileid": "https://r2.ropensci.org/8a64c63ffd5eda697307854235c9472341d980aaa72f617040d2cbe031c6694c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/patterninstitute/actions/runs/27937841642"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-06-22T07:58:55.000Z",
      "commit": "4e746e319e67d53f4722794148e6b03299e4ad72",
      "fileid": "https://r2.ropensci.org/227e86734acbf252ab5db2fff90bd446a39f5aeb3ed099ce69eb4280fa69c76d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/patterninstitute/actions/runs/27937841642"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-06-22T07:59:02.000Z",
      "commit": "4e746e319e67d53f4722794148e6b03299e4ad72",
      "fileid": "https://r2.ropensci.org/2f5aad5ecf6281221089b335d584a9f698d4f933b553e637336e8e544dca73b4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/patterninstitute/actions/runs/27937841642"
    }
  ]
}