{
  "_id": "69d4c89d10581d1350dbe4c9",
  "Package": "webseq",
  "Type": "Package",
  "Title": "Access data from biological sequence databases like NCBI, ENA,\nMGnify",
  "Description": "This package interacts with online biological sequence\ndatabases. It provides functions to search for sequences,\nconvert identifiers and download sequences and associated\nmetadata.",
  "Version": "0.1",
  "Date": "2022-01-05",
  "Author": "Tamas Stirling",
  "Maintainer": "Tamas Stirling <stirling.tamas@gmail.com>",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev",
  "Repository": "https://r-multiverse.r-universe.dev",
  "Date/Publication": "2024-01-17 08:49:50 UTC",
  "RemoteUrl": "https://github.com/stitam/webseq",
  "RemoteRef": "v0.1.0",
  "RemoteSha": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-04-07 08:46:05 UTC",
    "User": "root"
  },
  "MD5sum": "e2671762713ede1b4a07eab23d770be9",
  "_user": "r-multiverse",
  "_type": "src",
  "_file": "webseq_0.1.tar.gz",
  "_fileid": "ab5b6ce09a259e00191d7e14d474856667c9a32a85e9d04d8abc716e931a5c4a",
  "_filesize": 160864,
  "_sha256": "ab5b6ce09a259e00191d7e14d474856667c9a32a85e9d04d8abc716e931a5c4a",
  "_created": "2026-04-07T08:46:05.000Z",
  "_published": "2026-04-07T09:04:29.916Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 70213268219,
      "time": 185,
      "config": "linux-devel-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6302088611"
    },
    {
      "job": 70213268234,
      "time": 201,
      "config": "linux-release-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6302092275"
    },
    {
      "job": 70213268187,
      "time": 148,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6302331021"
    },
    {
      "job": 70213268259,
      "time": 159,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6302321227"
    },
    {
      "job": 70212711023,
      "time": 247,
      "config": "source",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6302036896"
    },
    {
      "job": 70213268110,
      "time": 125,
      "config": "wasm-release",
      "r": "4.5.1",
      "check": "OK",
      "artifact": "6302071895"
    },
    {
      "job": 70213268201,
      "time": 148,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "6302078050"
    },
    {
      "job": 70213268210,
      "time": 160,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6302081343"
    },
    {
      "job": 70213268173,
      "time": 176,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6302085913"
    }
  ],
  "_buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/24072493216",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/stitam/webseq",
  "_commit": {
    "id": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1",
    "author": "Tamás Stirling <49147718+stitam@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #51 from stitam/webhis2\n\nDo not use web histories by default with ncbi_link_uid()",
    "time": 1705481390
  },
  "_maintainer": {
    "name": "Tamas Stirling",
    "email": "stirling.tamas@gmail.com",
    "login": "stitam",
    "orcid": "0000-0002-8964-6443",
    "uuid": 49147718
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "curl",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "rentrez",
      "role": "Imports"
    },
    {
      "package": "stringi",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "XML",
      "role": "Imports"
    },
    {
      "package": "xml2",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "stitam",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "stitam",
      "count": 256,
      "uuid": 49147718
    }
  ],
  "_userbio": {
    "uuid": 161461790,
    "type": "organization",
    "name": "R-multiverse",
    "description": "A community-curated collection of R package releases, powered by R-universe"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/webseq"
  },
  "_devurl": "https://github.com/stitam/webseq",
  "_searchresults": 1,
  "_rbuild": "4.5.3",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/webseq.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "ena_query",
    "extract_accn",
    "flag_files",
    "mgnify_endpoints",
    "mgnify_instance",
    "mgnify_list",
    "ncbi_download_genome",
    "ncbi_get_meta",
    "ncbi_link_uid",
    "ncbi_parse",
    "ncbi_parse_assembly_xml",
    "ncbi_parse_biosample_txt",
    "parse_gb_header",
    "parse_report"
  ],
  "_datasets": [
    {
      "name": "examples",
      "title": "Examples",
      "object": "examples",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ena_query",
      "title": "Retrieve sequences from ENA",
      "topics": [
        "ena_query"
      ]
    },
    {
      "page": "examples",
      "title": "Examples",
      "topics": [
        "examples"
      ]
    },
    {
      "page": "extract_accn",
      "title": "Extract Accession Numbers from a parsed assembly report",
      "topics": [
        "extract_accn"
      ]
    },
    {
      "page": "flag_files",
      "title": "Flag files to keep for analysis",
      "topics": [
        "flag_files"
      ]
    },
    {
      "page": "mgnify_endpoints",
      "title": "MGnify endpoints",
      "topics": [
        "mgnify_endpoints"
      ]
    },
    {
      "page": "mgnify_instance",
      "title": "Search for a specific entry in MGnify",
      "topics": [
        "mgnify_instance"
      ]
    },
    {
      "page": "mgnify_list",
      "title": "Retrieve a list of instances from MGnify",
      "topics": [
        "mgnify_list"
      ]
    },
    {
      "page": "ncbi_download_genome",
      "title": "Download Genomes from NCBI",
      "topics": [
        "ncbi_download_genome"
      ]
    },
    {
      "page": "ncbi_get_meta",
      "title": "Get sequence metadata from NCBI",
      "topics": [
        "ncbi_get_meta"
      ]
    },
    {
      "page": "ncbi_get_uid",
      "title": "Get UID-s from NCBI databases",
      "topics": [
        "ncbi_get_uid"
      ]
    },
    {
      "page": "ncbi_link_uid",
      "title": "Link UID-s from one NCBI database to another",
      "topics": [
        "ncbi_link_uid"
      ]
    },
    {
      "page": "ncbi_meta_assembly",
      "title": "Retrieve NCBI Assembly metadata",
      "topics": [
        "ncbi_meta_assembly"
      ]
    },
    {
      "page": "ncbi_parse",
      "title": "Parse NCBI sequence metadata",
      "topics": [
        "ncbi_parse"
      ]
    },
    {
      "page": "ncbi_parse_assembly_xml",
      "title": "Parse NCBI assembly metadata",
      "topics": [
        "ncbi_parse_assembly_xml"
      ]
    },
    {
      "page": "ncbi_parse_biosample_txt",
      "title": "Parse NCBI BioSample metadata",
      "topics": [
        "ncbi_parse_biosample_txt"
      ]
    },
    {
      "page": "ncbi_parse_biosample_xml",
      "title": "Parse NCBI BioSample metadata",
      "topics": [
        "ncbi_parse_biosample_xml"
      ]
    },
    {
      "page": "parse_gb_header",
      "title": "Parse headers from GenBank files",
      "topics": [
        "parse_gb_header"
      ]
    },
    {
      "page": "parse_report",
      "title": "Parse assembly reports",
      "topics": [
        "parse_report"
      ]
    }
  ],
  "_readme": "https://github.com/stitam/webseq/raw/v0.1.0/README.md",
  "_rundeps": [
    "askpass",
    "cli",
    "cpp11",
    "curl",
    "dplyr",
    "generics",
    "glue",
    "httr",
    "jsonlite",
    "lifecycle",
    "magrittr",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "purrr",
    "R6",
    "Rcpp",
    "rentrez",
    "rlang",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XML",
    "xml2"
  ],
  "_vignettes": [
    {
      "source": "ncbi.Rmd",
      "filename": "ncbi.html",
      "title": "NCBI",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Download genome assemblies",
        "Download metadata",
        "Parse metadata files"
      ],
      "created": "2023-08-23 18:06:14",
      "modified": "2023-12-10 12:18:12",
      "commits": 4
    }
  ],
  "_score": 3.1760912590556813,
  "_indexed": false,
  "_nocasepkg": "webseq",
  "_universes": [
    "r-multiverse"
  ],
  "_indexurl": "https://stitam.r-universe.dev/webseq",
  "_binaries": [
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1",
      "date": "2026-04-07T08:48:12.000Z",
      "distro": "noble",
      "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1",
      "fileid": "b9e81584fe198b9f9f2b75cf2fa7b09c37e014d2d9b3ade3c802e3f3f89a185d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/24072493216"
    },
    {
      "r": "4.5.3",
      "os": "linux",
      "version": "0.1",
      "date": "2026-04-07T08:48:15.000Z",
      "distro": "noble",
      "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1",
      "fileid": "9fcc5bd8aebbe8094f70c10505a964f8028938b4a17a0ebd97dfda32745dbf76",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/24072493216"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1",
      "date": "2026-04-07T09:02:44.000Z",
      "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1",
      "fileid": "290fbc2fc73093675359a05fe4d3fd1366610dd84220232a2fdf710d82e2c51e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/24072493216"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1",
      "date": "2026-04-07T09:02:05.000Z",
      "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1",
      "fileid": "50c3db06086b9a8f99e2876807b157c07e15c00a9d4a2cdd3e0f8ee8f46e0b0c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/24072493216"
    },
    {
      "r": "4.5.1",
      "os": "wasm",
      "version": "0.1",
      "date": "2026-04-07T08:48:24.000Z",
      "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1",
      "fileid": "5cb75996fa56200b5715960e42be0e8818e36c61fd5189f06fd15364f417302c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/24072493216"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1",
      "date": "2026-04-07T08:47:15.000Z",
      "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1",
      "fileid": "ea15a42af4ab7cd5d42d6d91347982c95d7c53c6b66d2b8ad3e38325f2746631",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/24072493216"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1",
      "date": "2026-04-07T08:47:41.000Z",
      "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1",
      "fileid": "1aab3cf6d7704d507c2506791011e545cf53658c7e6445fbc3bf6cfcd1943d29",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/24072493216"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1",
      "date": "2026-04-07T08:47:51.000Z",
      "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1",
      "fileid": "3290b28a5f5906e353be91e1b357da01e7922a7f7e985597420b513f0550dd1c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/24072493216"
    }
  ]
}