{
  "_id": "6ac3e13834f9a32edea23150",
  "Package": "phiperio",
  "Title": "PhIP-Seq Data Import and Validation Tools",
  "Version": "0.6.1",
  "Authors@R": "c(\nperson(\n\"Mateusz\", \"Kolek\",\nemail = \"mati.kolek13@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-6470-4830\")\n),\nperson(\n\"Alon\", \"Alexander\",\nemail = \"a.alexander@umcg.nl\",\nrole = c(\"ctb\", \"cph\"),\ncomment = \"advised on package scope and data storage design\"\n)\n)",
  "Description": "Provides utilities to import, validate, and manage\nPhIP-Seq datasets, including standardized conversion pipelines,\ndata checks, and access to cached peptide metadata.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/Polymerase3/phiperio,\nhttps://polymerase3.github.io/phiperio/",
  "BugReports": "https://github.com/Polymerase3/phiperio/issues",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libicu-dev xz-utils",
  "Repository": "https://polymerase3.r-universe.dev",
  "Date/Publication": "2026-10-05 13:07:23 UTC",
  "RemoteUrl": "https://github.com/Polymerase3/phiperio",
  "RemoteRef": "main",
  "RemoteSha": "2a8d8f2fa5cf2579f5999c03d9c06106504b81f5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-05 17:06:54 UTC",
    "User": "root"
  },
  "Author": "Mateusz Kolek [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-6470-4830>),\nAlon Alexander [ctb, cph] (advised on package scope and data storage\ndesign)",
  "Maintainer": "Mateusz Kolek <mati.kolek13@gmail.com>",
  "_user": "polymerase3",
  "_type": "src",
  "_file": "phiperio_0.6.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/c0b8c52fa8bade48483e7dd8a5bde9f7e23cd2d891fb13862d116d611995387d",
  "_filesize": 953570,
  "_sha256": "c0b8c52fa8bade48483e7dd8a5bde9f7e23cd2d891fb13862d116d611995387d",
  "_expires": "2027-01-13T17:41:10.000Z",
  "_created": "2026-10-05T17:06:54.000Z",
  "_published": "2026-10-05T17:41:12.347Z",
  "_jobs": [
    {
      "job": 111884714715,
      "time": 156,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11361005450"
    },
    {
      "job": 111884714535,
      "time": 155,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11360094184"
    },
    {
      "job": 111884714649,
      "time": 212,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11362172340"
    },
    {
      "job": 111884714640,
      "time": 215,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11362395594"
    },
    {
      "job": 111883195792,
      "time": 211,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11359679973"
    },
    {
      "job": 111884714506,
      "time": 104,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11360955488"
    },
    {
      "job": 111884714973,
      "time": 122,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11360677665"
    },
    {
      "job": 111884714616,
      "time": 141,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11359404762"
    },
    {
      "job": 111884714763,
      "time": 186,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11360826841"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/polymerase3/actions/runs/37345539396",
  "_status": "success",
  "_upstream": "https://github.com/Polymerase3/phiperio",
  "_commit": {
    "id": "2a8d8f2fa5cf2579f5999c03d9c06106504b81f5",
    "author": "Mateusz Franciszek Kolek <78413933+Polymerase3@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #20 from Polymerase3/ci/phipflow-compat\n\nAdd phipflow compatibility check to CI",
    "time": 1791205643
  },
  "_maintainer": {
    "name": "Mateusz Kolek",
    "email": "mati.kolek13@gmail.com",
    "login": "polymerase3",
    "description": "Research software engineer in biostats/computational immunology (MD/PhD @ MedUni Vienna)",
    "uuid": 78413933,
    "orcid": "0000-0001-6470-4830"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "chk",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "DBI",
      "role": "Imports"
    },
    {
      "package": "dbplyr",
      "role": "Imports"
    },
    {
      "package": "digest",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "duckdb",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "withr",
      "role": "Imports"
    },
    {
      "package": "yaml",
      "role": "Imports"
    },
    {
      "package": "curl",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "mockery",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "polymerase3",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2026-06",
      "n": 36
    },
    {
      "week": "2026-28",
      "n": 2
    },
    {
      "week": "2026-36",
      "n": 1
    },
    {
      "week": "2026-37",
      "n": 3
    },
    {
      "week": "2026-41",
      "n": 3
    }
  ],
  "_tags": [],
  "_stars": 5,
  "_contributors": [
    {
      "user": "polymerase3",
      "count": 64,
      "uuid": 78413933
    }
  ],
  "_userbio": {
    "uuid": 78413933,
    "type": "user",
    "name": "Mateusz Franciszek Kolek",
    "followers": 0,
    "description": "Research software engineer in biostats/computational immunology (MD/PhD @ MedUni Vienna)"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phiperio"
  },
  "_devurl": "https://github.com/polymerase3/phiperio",
  "_pkgdown": "https://polymerase3.github.io/phiperio/",
  "_searchresults": 14,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/phiperio.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_cranurl": false,
  "_exports": [
    "add_exist",
    "convert_legacy",
    "convert_standard",
    "create_data",
    "detect_peptide_libraries",
    "expand_data",
    "export_parquet",
    "get_counts",
    "get_example_path",
    "get_meta",
    "get_peptide_library",
    "load_example_data"
  ],
  "_help": [
    {
      "page": "add_exist",
      "title": "Ensure an existence flag (all ones) on 'data_long'",
      "topics": [
        "add_exist"
      ]
    },
    {
      "page": "close.phip_data",
      "title": "Close phip_data connections",
      "topics": [
        "close.phip_data"
      ]
    },
    {
      "page": "convert_legacy",
      "title": "Convert legacy Carlos-style input to a modern *phip_data* object",
      "topics": [
        "convert_legacy"
      ]
    },
    {
      "page": "convert_standard",
      "title": "Convert raw PhIP-Seq output into a 'phip_data' object",
      "topics": [
        "convert_standard"
      ]
    },
    {
      "page": "create_data",
      "title": "Construct a *phip_data* object",
      "topics": [
        "create_data"
      ]
    },
    {
      "page": "detect_peptide_libraries",
      "title": "Detect the peptide libraries a set of peptides belongs to",
      "topics": [
        "detect_peptide_libraries"
      ]
    },
    {
      "page": "expand_data",
      "title": "Expand to a full 'sample_id * peptide_id' grid",
      "topics": [
        "expand_data"
      ]
    },
    {
      "page": "export_parquet",
      "title": "Export a phip_data Table to Parquet",
      "topics": [
        "export_parquet"
      ]
    },
    {
      "page": "get_counts",
      "title": "Retrieve the main PhIP-Seq counts table",
      "topics": [
        "get_counts"
      ]
    },
    {
      "page": "get_example_path",
      "title": "Path to example PhIP-Seq datasets shipped with phiperio",
      "topics": [
        "get_example_path"
      ]
    },
    {
      "page": "get_meta",
      "title": "Retrieve the metadata list",
      "topics": [
        "get_meta"
      ]
    },
    {
      "page": "get_peptide_library",
      "title": "Retrieve the peptide metadata table into DuckDB, forcing atomic types",
      "topics": [
        "get_peptide_library"
      ]
    },
    {
      "page": "load_example_data",
      "title": "Load Example PhIP-Seq Dataset as <phip_data>",
      "topics": [
        "load_example_data"
      ]
    },
    {
      "page": "merge.phip_data",
      "title": "Merge or join a 'phip_data' object",
      "topics": [
        "merge.phip_data"
      ]
    },
    {
      "page": "phip_data_join",
      "title": "dplyr joins for 'phip_data'",
      "topics": [
        "anti_join.phip_data",
        "full_join.phip_data",
        "inner_join.phip_data",
        "left_join.phip_data",
        "phip_data_join",
        "right_join.phip_data",
        "semi_join.phip_data"
      ]
    }
  ],
  "_readme": "https://github.com/Polymerase3/phiperio/raw/main/README.md",
  "_rundeps": [
    "blob",
    "chk",
    "cli",
    "cpp11",
    "DBI",
    "dbplyr",
    "digest",
    "dplyr",
    "duckdb",
    "generics",
    "glue",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "rlang",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "importing-long-tidy-data.Rmd",
      "filename": "importing-long-tidy-data.html",
      "title": "Importing cross-sectional and longitudinal tidy data with phiperio",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Key concepts (read first)",
        "Cross-sectional workflow (simpler)",
        "Longitudinal workflow (subjects with multiple samples)",
        "Tips and gotchas",
        "Using the built-in example"
      ],
      "created": "2026-02-04 11:48:13",
      "modified": "2026-10-05 08:30:11",
      "commits": 2
    },
    {
      "source": "importing-legacy-data.Rmd",
      "filename": "importing-legacy-data.html",
      "title": "Importing legacy PhIP-Seq data (convert_legacy)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What this covers",
        "Cross-sectional: one sample per subject",
        "Longitudinal: multiple samples per subject",
        "Key points"
      ],
      "created": "2026-02-04 13:42:08",
      "modified": "2026-02-04 13:42:08",
      "commits": 1
    },
    {
      "source": "importing-multiple-files.Rmd",
      "filename": "importing-multiple-files.html",
      "title": "Importing multiple files with phiperio",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "1. Create a bunch of example files",
        "2. Inspect one file so you know what’s inside",
        "3. Import all files in one call",
        "4. Derive run_id and plate_id from sample_id",
        "Summary"
      ],
      "created": "2026-02-04 13:42:08",
      "modified": "2026-02-04 13:42:08",
      "commits": 1
    }
  ],
  "_score": 5.19728055812562,
  "_indexed": true,
  "_nocasepkg": "phiperio",
  "_universes": [
    "polymerase3"
  ],
  "_previous": "0.5.5",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.6.1",
      "date": "2026-10-05T17:09:04.000Z",
      "distro": "resolute",
      "commit": "2a8d8f2fa5cf2579f5999c03d9c06106504b81f5",
      "fileid": "https://r2.ropensci.org/1caa3fba3bdc36c272f20ef706a594565e49a77989ceea0cb1cc47f7db1720f7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/polymerase3/actions/runs/37345539396"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.6.1",
      "date": "2026-10-05T17:09:07.000Z",
      "distro": "resolute",
      "commit": "2a8d8f2fa5cf2579f5999c03d9c06106504b81f5",
      "fileid": "https://r2.ropensci.org/4cdd15d2a47c063c1631db5598531e52cfd58ebb484ce1443c9b2ecfe776aa2d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/polymerase3/actions/runs/37345539396"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.6.1",
      "date": "2026-10-05T17:39:37.000Z",
      "commit": "2a8d8f2fa5cf2579f5999c03d9c06106504b81f5",
      "fileid": "https://r2.ropensci.org/11be8530b05a9ef18fe3380f597c2a4dfb03cc02fd16b44518f1b7a827ac3fd8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/polymerase3/actions/runs/37345539396"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.6.1",
      "date": "2026-10-05T17:33:55.000Z",
      "commit": "2a8d8f2fa5cf2579f5999c03d9c06106504b81f5",
      "fileid": "https://r2.ropensci.org/753c537659ed3987a26e9f9b79938f9a6127890b08d372e6c628f1b4503532f1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/polymerase3/actions/runs/37345539396"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.6.1",
      "date": "2026-10-05T17:09:00.000Z",
      "commit": "2a8d8f2fa5cf2579f5999c03d9c06106504b81f5",
      "fileid": "https://r2.ropensci.org/03120a33b6ca48a9b29cb79494f6ce16910a1a5c543884d1c4a5dcf61215280c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/polymerase3/actions/runs/37345539396"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.6.1",
      "date": "2026-10-05T17:08:15.000Z",
      "commit": "2a8d8f2fa5cf2579f5999c03d9c06106504b81f5",
      "fileid": "https://r2.ropensci.org/3cd442b5d1c01fa07393d5786ddbdba1310ad4bf0c9d6dd212c9423de4eefa3c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/polymerase3/actions/runs/37345539396"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.6.1",
      "date": "2026-10-05T17:08:29.000Z",
      "commit": "2a8d8f2fa5cf2579f5999c03d9c06106504b81f5",
      "fileid": "https://r2.ropensci.org/2d6b8e2c27c950f8e88ae2f9b2df4c1d171c5acda12dbe87ff2488045fddaf4f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/polymerase3/actions/runs/37345539396"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.6.1",
      "date": "2026-10-05T17:09:20.000Z",
      "commit": "2a8d8f2fa5cf2579f5999c03d9c06106504b81f5",
      "fileid": "https://r2.ropensci.org/4b326719bed162746478897eb807746c3b9122b5ebf3034109ed593f6af9ef9f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/polymerase3/actions/runs/37345539396"
    }
  ]
}