{
  "_id": "6a1ae7d71d7bb097a09f1690",
  "Package": "Pirat",
  "Type": "Package",
  "Title": "Precursor or Peptide Imputation under Random Truncation",
  "Description": "Pirat enables the imputation of missing values (either\nMNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a\npenalized maximum likelihood strategy. It does not require any\nparameter tuning, it models the instrument censorship from the\ndata available. It accounts for sibling peptides correlations\nand it can leverage complementary transcriptomics measurements.",
  "Version": "1.6.0",
  "Authors@R": "c(person(given = \"Lucas\",\nfamily = \"Etourneau\",\nemail = \"lucas.etourneau@gmail.com\",\nrole = c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0002-8670-808X\")),\nperson(given = \"Laura\",\nfamily = \"Fancello\",\nemail = \" laura.fancello@cea.fr\",\nrole = c(\"aut\")),\nperson(given = \"Manon\",\nfamily = \"Gaudin\",\nemail = \"manon.gaudin@cea.fr\",\nrole = c(\"aut\")),\nperson(given = \"Samuel\",\nfamily = \"Wieczorek\",\nemail = \"samuel.wieczorek@cea.fr\",\nrole = c(\"aut\"),\ncomment = c(ORCID=\"0000-0002-5016-1203\")),\nperson(given = \"Nelle\",\nfamily = \"Varoquaux\",\nemail = \" nelle.varoquaux@univ-grenoble-alpes.fr\",\nrole = c(\"aut\")),\nperson(given = \"Thomas\",\nfamily = \"Burger\",\nemail = \"thomas.burger@cea.fr\",\nrole = c(\"aut\")))",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "biocViews": "Proteomics, MassSpectrometry, Preprocessing, Software",
  "RoxygenNote": "7.3.2",
  "BiocViews": "Proteomics, MassSpectrometry",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/edyp-lab/Pirat",
  "BugReports": "https://github.com/edyp-lab/Pirat/issues",
  "StagedInstall": "no",
  "Config/pak/sysreqs": "libpng-dev python3 zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:03:12 UTC",
  "RemoteUrl": "https://github.com/bioc/Pirat",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "567340b9e3a1f37e394637b228a7ee7c7573ff73",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:25:01 UTC",
    "User": "root"
  },
  "Author": "Lucas Etourneau [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-8670-808X>),\nLaura Fancello [aut],\nManon Gaudin [aut],\nSamuel Wieczorek [aut] (ORCID: <https://orcid.org/0000-0002-5016-1203>),\nNelle Varoquaux [aut],\nThomas Burger [aut]",
  "Maintainer": "Lucas Etourneau <lucas.etourneau@gmail.com>",
  "MD5sum": "63741985c65b73825caff4ac8d6cc999",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "Pirat_1.6.0.tar.gz",
  "_fileid": "765927d6968b4404111270df14bb5e3d48e8479b3b26a86c75acc86b7bc74191",
  "_filesize": 2603033,
  "_sha256": "765927d6968b4404111270df14bb5e3d48e8479b3b26a86c75acc86b7bc74191",
  "_created": "2026-05-30T09:25:01.000Z",
  "_published": "2026-05-30T13:36:23.748Z",
  "_jobs": [
    {
      "job": 78639517458,
      "time": 168,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307223550"
    },
    {
      "job": 78639517453,
      "time": 876,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307294370"
    },
    {
      "job": 78639517464,
      "time": 860,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307294911"
    },
    {
      "job": 78639517466,
      "time": 723,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308558523"
    },
    {
      "job": 78639517454,
      "time": 702,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308555864"
    },
    {
      "job": 78638692975,
      "time": 851,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307161820"
    },
    {
      "job": 78639517459,
      "time": 141,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307222166"
    },
    {
      "job": 78639517470,
      "time": 346,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307242317"
    },
    {
      "job": 78639517455,
      "time": 341,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307238939"
    },
    {
      "job": 78639517468,
      "time": 336,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307239157"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680008730",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Pirat",
  "_commit": {
    "id": "567340b9e3a1f37e394637b228a7ee7c7573ff73",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777381392
  },
  "_maintainer": {
    "name": "Lucas Etourneau",
    "email": "lucas.etourneau@gmail.com",
    "login": "lucas-et",
    "description": "",
    "uuid": 38471671,
    "orcid": "0000-0002-8670-808X"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "basilisk",
      "role": "Imports"
    },
    {
      "package": "reticulate",
      "role": "Imports"
    },
    {
      "package": "progress",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "invgamma",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-22",
      "n": 5
    },
    {
      "week": "2025-23",
      "n": 1
    },
    {
      "week": "2025-24",
      "n": 1
    },
    {
      "week": "2025-25",
      "n": 1
    },
    {
      "week": "2025-31",
      "n": 1
    },
    {
      "week": "2025-33",
      "n": 4
    },
    {
      "week": "2025-35",
      "n": 2
    },
    {
      "week": "2025-36",
      "n": 2
    },
    {
      "week": "2025-38",
      "n": 2
    },
    {
      "week": "2025-39",
      "n": 3
    },
    {
      "week": "2025-40",
      "n": 3
    },
    {
      "week": "2025-41",
      "n": 2
    },
    {
      "week": "2025-42",
      "n": 1
    },
    {
      "week": "2025-43",
      "n": 6
    },
    {
      "week": "2025-45",
      "n": 7
    },
    {
      "week": "2025-46",
      "n": 3
    },
    {
      "week": "2025-47",
      "n": 2
    },
    {
      "week": "2025-48",
      "n": 2
    },
    {
      "week": "2026-09",
      "n": 3
    },
    {
      "week": "2026-11",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.7.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.6.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "proteomics",
    "massspectrometry",
    "preprocessing",
    "software",
    "prostar2"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "samwieczorek",
      "count": 182,
      "uuid": 2912670
    },
    {
      "user": "lucas-et",
      "count": 71,
      "uuid": 38471671
    },
    {
      "user": "jwokaty",
      "count": 6,
      "uuid": 1744257
    },
    {
      "user": "pomkokca",
      "count": 3,
      "uuid": 144104844
    },
    {
      "user": "samuelwieczorek",
      "count": 1,
      "uuid": 71639216
    },
    {
      "user": "lshep",
      "count": 1,
      "uuid": 18724380
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 278,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Pirat"
  },
  "_devurl": "https://github.com/edyp-lab/pirat",
  "_searchresults": 9,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/Pirat.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/edyp-lab/pirat",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "envPirat",
    "estimate_gamma",
    "estimate_psi_df",
    "get_indexes_embedded_prots",
    "impute_block_llk_reset",
    "impute_block_llk_reset_PG",
    "impute_from_blocks",
    "my_pipeline_llkimpute",
    "pipeline_llkimpute",
    "pirat2SE",
    "plot_pep_correlations",
    "plot2hists",
    "rm_pg_from_idx_merge_pg",
    "split_large_pg",
    "split_large_pg_PG",
    "wrapper_pipeline_llkimpute"
  ],
  "_datasets": [
    {
      "name": "ropers",
      "title": "Ropers dataset",
      "object": "ropers",
      "file": "ropers.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "subbouyssie",
      "title": "Sub-Bouyssie dataset",
      "object": "subbouyssie",
      "file": "subbouyssie.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "subropers",
      "title": "Sub-Ropers dataset",
      "object": "subropers",
      "file": "subropers.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "envPirat",
      "title": "Creates a BasiliskEnvironment class",
      "topics": [
        "envPirat"
      ]
    },
    {
      "page": "estimate_gamma",
      "title": "Estimate missingness parameters Gamma",
      "topics": [
        "estimate_gamma"
      ]
    },
    {
      "page": "estimate_psi_df",
      "title": "Estimate psi and degrees of freedom",
      "topics": [
        "estimate_psi_df"
      ]
    },
    {
      "page": "get_indexes_embedded_prots",
      "title": "Indexes of PGs embedded in each others",
      "topics": [
        "get_indexes_embedded_prots"
      ]
    },
    {
      "page": "impute_block_llk_reset",
      "title": "Impute each PG.",
      "topics": [
        "impute_block_llk_reset"
      ]
    },
    {
      "page": "impute_block_llk_reset_PG",
      "title": "Impute each PG.",
      "topics": [
        "impute_block_llk_reset_PG"
      ]
    },
    {
      "page": "impute_from_blocks",
      "title": "Impute abundance table from PGs results",
      "topics": [
        "impute_from_blocks"
      ]
    },
    {
      "page": "pipeline_llkimpute",
      "title": "Pirat imputation function",
      "topics": [
        "my_pipeline_llkimpute",
        "pipeline_llkimpute"
      ]
    },
    {
      "page": "pirat2SE",
      "title": "COnvert Pirat dataset to SummarizedExperiment",
      "topics": [
        "pirat2SE"
      ]
    },
    {
      "page": "plot_pep_correlations",
      "title": "Empirical density of peptide correlations",
      "topics": [
        "plot_pep_correlations"
      ]
    },
    {
      "page": "plot2hists",
      "title": "Plot 2 histograms",
      "topics": [
        "plot2hists"
      ]
    },
    {
      "page": "rm_pg_from_idx_merge_pg",
      "title": "Remove PGs by index and merge",
      "topics": [
        "rm_pg_from_idx_merge_pg"
      ]
    },
    {
      "page": "ropers",
      "title": "Ropers dataset",
      "topics": [
        "ropers"
      ]
    },
    {
      "page": "split_large_pg",
      "title": "Split too large PGs",
      "topics": [
        "split_large_pg"
      ]
    },
    {
      "page": "split_large_pg_PG",
      "title": "Splits too large PGs in proteogenomics context",
      "topics": [
        "split_large_pg_PG"
      ]
    },
    {
      "page": "subbouyssie",
      "title": "Sub-Bouyssie dataset",
      "topics": [
        "subbouyssie"
      ]
    },
    {
      "page": "subropers",
      "title": "Sub-Ropers dataset",
      "topics": [
        "subropers"
      ]
    },
    {
      "page": "wrapper_pipeline_llkimpute",
      "title": "Imputation method using SummarizedExperiment dataset",
      "topics": [
        "wrapper_pipeline_llkimpute"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Pirat/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "basilisk",
    "Biobase",
    "BiocGenerics",
    "cli",
    "cpp11",
    "crayon",
    "DelayedArray",
    "dir.expiry",
    "farver",
    "filelock",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "here",
    "hms",
    "invgamma",
    "IRanges",
    "isoband",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppTOML",
    "reticulate",
    "rlang",
    "rprojroot",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SparseArray",
    "SummarizedExperiment",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "Pirat.Rmd",
      "filename": "Pirat.html",
      "title": "Pirat",
      "author": "Lucas Etourneau, Samuel Wieczorek",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Standard imputation with Pirat",
        "Intra-PG correlation analysis",
        "Pirat extensions",
        "-2, the 2-peptide rule",
        "-S, samples-wise correlations",
        "-T, transcriptomic integration",
        "5. Session info",
        "References"
      ],
      "created": "2024-03-13 13:27:44",
      "modified": "2026-02-26 19:14:56",
      "commits": 17
    }
  ],
  "_score": 6.19728055812562,
  "_indexed": false,
  "_nocasepkg": "pirat",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/Pirat",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.6.0",
      "date": "2026-05-30T09:36:17.000Z",
      "distro": "noble",
      "commit": "567340b9e3a1f37e394637b228a7ee7c7573ff73",
      "fileid": "f0a4ffbbad270727fedcfda8fe33c69f34eed31426572758af93b44088e1bfed",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680008730"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.6.0",
      "date": "2026-05-30T09:36:12.000Z",
      "distro": "noble",
      "commit": "567340b9e3a1f37e394637b228a7ee7c7573ff73",
      "fileid": "e7587d8f6deaf41811c59111e10dc0f6c1ccc3e41c1575195044e7176eec56d5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680008730"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.6.0",
      "date": "2026-05-30T13:25:18.000Z",
      "commit": "567340b9e3a1f37e394637b228a7ee7c7573ff73",
      "fileid": "8165a3a8961d5f5624638041175cb6c912e3a834e6456288b99f2206614b7f3d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680008730"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.6.0",
      "date": "2026-05-30T13:25:18.000Z",
      "commit": "567340b9e3a1f37e394637b228a7ee7c7573ff73",
      "fileid": "8d4e14dfa8108de71bb1fac6a90d524331e8cf65d37df76b29e2523fe820845f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680008730"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.6.0",
      "date": "2026-05-30T09:36:07.000Z",
      "commit": "567340b9e3a1f37e394637b228a7ee7c7573ff73",
      "fileid": "075eb8374f2da4b883887d944cab0b73332acf4a290b355250016117fda3b4f1",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680008730"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.6.0",
      "date": "2026-05-30T09:35:02.000Z",
      "commit": "567340b9e3a1f37e394637b228a7ee7c7573ff73",
      "fileid": "e0f665b54aceb66b53b860fedd7fb1b067b6547cf30bfb348c28d8be115b182f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680008730"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.6.0",
      "date": "2026-05-30T09:34:25.000Z",
      "commit": "567340b9e3a1f37e394637b228a7ee7c7573ff73",
      "fileid": "8d86d7ead82dd97d655ec490543b75600a2ef2a29114068345d4dd70ccc2647c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680008730"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.6.0",
      "date": "2026-05-30T09:34:32.000Z",
      "commit": "567340b9e3a1f37e394637b228a7ee7c7573ff73",
      "fileid": "38a8ea11fe76a3e71450c4ea569db46cfd25a23f4282af747b613d047f145530",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680008730"
    }
  ]
}