{
  "_id": "6aabcd8b3d719c1f8406f04f",
  "Package": "proDA",
  "Type": "Package",
  "Title": "Differential Abundance Analysis of Label-Free Mass Spectrometry\nData",
  "Version": "1.27.0",
  "Authors@R": "c(person(\"Constantin\", \"Ahlmann-Eltze\", email = \"artjom31415@googlemail.com\", \nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-3762-068X\")),\nperson(\"Simon\", \"Anders\", email=\"s.anders@zmbh.uni-heidelberg.de\",\nrole=\"ths\", comment = c(ORCID = \"0000-0003-4868-1805\")))",
  "Description": "Account for missing values in label-free mass spectrometry\ndata without imputation. The package implements a probabilistic\ndropout model that ensures that the information from observed\nand missing values are properly combined. It adds empirical\nBayesian priors to increase power to detect differentially\nabundant proteins.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.0",
  "URL": "https://github.com/const-ae/proDA",
  "BugReports": "https://github.com/const-ae/proDA/issues",
  "biocViews": "Proteomics, MassSpectrometry, DifferentialExpression,\nBayesian, Regression, Software, Normalization, QualityControl",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:50:37 UTC",
  "RemoteUrl": "https://github.com/bioc/proDA",
  "RemoteRef": "HEAD",
  "RemoteSha": "ae2d3b17498a68ebd3a5a29e4e5afa4bd2883134",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-17 10:04:34 UTC",
    "User": "root"
  },
  "Author": "Constantin Ahlmann-Eltze [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3762-068X>),\nSimon Anders [ths] (ORCID: <https://orcid.org/0000-0003-4868-1805>)",
  "Maintainer": "Constantin Ahlmann-Eltze <artjom31415@googlemail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "proDA_1.27.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b6e9c0d80480c0b5430a27063b7ee564c561de4d06aa5bd95f65e59529b1499b",
  "_filesize": 1178463,
  "_sha256": "b6e9c0d80480c0b5430a27063b7ee564c561de4d06aa5bd95f65e59529b1499b",
  "_expires": "2026-12-26T11:22:49.000Z",
  "_created": "2026-09-17T10:04:34.000Z",
  "_published": "2026-09-17T11:22:51.676Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 9
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35207999802",
  "_status": "success",
  "_upstream": "https://github.com/bioc/proDA",
  "_commit": {
    "id": "ae2d3b17498a68ebd3a5a29e4e5afa4bd2883134",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380637
  },
  "_maintainer": {
    "name": "Constantin Ahlmann-Eltze",
    "email": "artjom31415@googlemail.com",
    "login": "const-ae",
    "bluesky": "@const-ae.bsky.social",
    "orcid": "0000-0002-3762-068X",
    "description": "Postdoc, Biostats, R",
    "uuid": 5359014
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 105160413768,
      "time": 225,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10491197838"
    },
    {
      "job": 105160413728,
      "time": 410,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10490622675"
    },
    {
      "job": 105160413877,
      "time": 393,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10490967441"
    },
    {
      "job": 105160413631,
      "time": 206,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10494670336"
    },
    {
      "job": 105160413703,
      "time": 239,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10494945309"
    },
    {
      "job": 105158516022,
      "time": 382,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10491451165"
    },
    {
      "job": 105160413614,
      "time": 167,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10491396181"
    },
    {
      "job": 105160413702,
      "time": 293,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10490913472"
    },
    {
      "job": 105160413838,
      "time": 306,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10491117021"
    },
    {
      "job": 105160413679,
      "time": 298,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10491142039"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "extraDistr",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 2.1.0",
      "role": "Suggests"
    },
    {
      "package": "MSnbase",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "stringr",
      "role": "Suggests"
    },
    {
      "package": "readr",
      "role": "Suggests"
    },
    {
      "package": "tidyr",
      "role": "Suggests"
    },
    {
      "package": "tibble",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "numDeriv",
      "role": "Suggests"
    },
    {
      "package": "pheatmap",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-14",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.27.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.26.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "proteomics",
    "massspectrometry",
    "differentialexpression",
    "bayesian",
    "regression",
    "software",
    "normalization",
    "qualitycontrol"
  ],
  "_stars": 24,
  "_contributors": [
    {
      "user": "const-ae",
      "count": 176,
      "uuid": 5359014
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 12,
      "uuid": 2746443
    },
    {
      "user": "simon-anders",
      "count": 8,
      "uuid": 12886712
    },
    {
      "user": "elena-krismer",
      "count": 2,
      "uuid": 70535771
    },
    {
      "user": "tnaake",
      "count": 2,
      "uuid": 7208089
    },
    {
      "user": "amackey",
      "count": 1,
      "uuid": 274736
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 467,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 589,
    "source": "https://www.bioconductor.org/packages/stats/bioc/proDA"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/const-ae/proda",
  "_searchresults": 130,
  "_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/proDA.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/const-ae/proda",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "abundances",
    "coefficient_variance_matrices",
    "coefficients",
    "convergence",
    "design",
    "dist_approx",
    "feature_parameters",
    "generate_synthetic_data",
    "hyper_parameters",
    "invprobit",
    "median_normalization",
    "pd_lm",
    "pd_row_f_test",
    "pd_row_t_test",
    "predict",
    "proDA",
    "reference_level",
    "result_names",
    "test_diff"
  ],
  "_help": [
    {
      "page": "cash-proDAFit-method",
      "title": "Fluent use of accessor methods",
      "topics": [
        "$,proDAFit-method",
        "$<-,proDAFit-method",
        ".DollarNames.proDAFit",
        "dollar_methods"
      ]
    },
    {
      "page": "abundances",
      "title": "Get the abundance matrix",
      "topics": [
        "abundances"
      ]
    },
    {
      "page": "accessor_methods",
      "title": "Get different features and elements of the 'proDAFit' object",
      "topics": [
        "abundances,proDAFit-method",
        "accessor_methods",
        "coefficients,proDAFit-method",
        "coefficient_variance_matrices,proDAFit-method",
        "convergence,proDAFit-method",
        "design,proDAFit-method",
        "feature_parameters,proDAFit-method",
        "hyper_parameters,proDAFit-method",
        "reference_level,proDAFit-method"
      ]
    },
    {
      "page": "coefficient_variance_matrices",
      "title": "Get the coefficients",
      "topics": [
        "coefficient_variance_matrices"
      ]
    },
    {
      "page": "coefficients",
      "title": "Get the coefficients",
      "topics": [
        "coefficients"
      ]
    },
    {
      "page": "convergence",
      "title": "Get the convergence information",
      "topics": [
        "convergence"
      ]
    },
    {
      "page": "dist_approx",
      "title": "Calculate an approximate distance for 'object'",
      "topics": [
        "dist_approx"
      ]
    },
    {
      "page": "dist_approx_impl",
      "title": "Distance method for 'proDAFit' object",
      "topics": [
        "dist_approx,ANY-method",
        "dist_approx,proDAFit-method",
        "dist_approx,SummarizedExperiment-method",
        "dist_approx_impl"
      ]
    },
    {
      "page": "feature_parameters",
      "title": "Get the feature parameters",
      "topics": [
        "feature_parameters"
      ]
    },
    {
      "page": "generate_synthetic_data",
      "title": "Generate a dataset according to the probabilistic dropout model",
      "topics": [
        "generate_synthetic_data"
      ]
    },
    {
      "page": "hyper_parameters",
      "title": "Get the hyper parameters",
      "topics": [
        "hyper_parameters"
      ]
    },
    {
      "page": "invprobit",
      "title": "Inverse probit function",
      "topics": [
        "invprobit"
      ]
    },
    {
      "page": "median_normalization",
      "title": "Column wise median normalization of the data matrix",
      "topics": [
        "median_normalization"
      ]
    },
    {
      "page": "pd_lm",
      "title": "Fit a single linear probabilistic dropout model",
      "topics": [
        "pd_lm"
      ]
    },
    {
      "page": "pd_row_t_test",
      "title": "Row-wise tests of difference using the probabilistic dropout model",
      "topics": [
        "pd_row_f_test",
        "pd_row_t_test"
      ]
    },
    {
      "page": "predict-proDAFit-method",
      "title": "Predict the parameters or values of additional proteins",
      "topics": [
        "predict,proDAFit-method"
      ]
    },
    {
      "page": "proDA",
      "title": "Main function to fit the probabilistic dropout model",
      "topics": [
        "proDA"
      ]
    },
    {
      "page": "proDA_package",
      "title": "proDA: Identify differentially abundant proteins in label-free mass spectrometry",
      "topics": [
        "proDA_package"
      ]
    },
    {
      "page": "proDAFit-class",
      "title": "proDA Class Definition",
      "topics": [
        ".proDAFit",
        "proDAFit-class"
      ]
    },
    {
      "page": "reference_level",
      "title": "Get the reference level",
      "topics": [
        "reference_level"
      ]
    },
    {
      "page": "result_names",
      "title": "Get the result_names",
      "topics": [
        "result_names"
      ]
    },
    {
      "page": "test_diff",
      "title": "Identify differentially abundant proteins",
      "topics": [
        "result_names,proDAFit-method",
        "test_diff"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/proDA/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "DelayedArray",
    "extraDistr",
    "generics",
    "GenomicRanges",
    "IRanges",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "Rcpp",
    "RcppArmadillo",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SparseArray",
    "SummarizedExperiment",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "data-import.Rmd",
      "filename": "data-import.html",
      "title": "Proteomics Data Import",
      "author": "Constantin Ahlmann-Eltze",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "MaxQuant File Overview",
        "Workflow",
        "Base R",
        "Tidyverse",
        "Session Info"
      ],
      "created": "2019-05-31 12:56:32",
      "modified": "2026-04-01 20:33:31",
      "commits": 6
    },
    {
      "source": "Introduction.Rmd",
      "filename": "Introduction.html",
      "title": "Introduction",
      "author": "Constantin Ahlmann-Eltze",
      "engine": "knitr::rmarkdown",
      "headings": [
        "proDA",
        "Installation",
        "Quickstart",
        "proDA Walkthrough",
        "Load Data",
        "Quality Control",
        "Fit the Probabilistic Dropout Model",
        "Identify Differential Abundance",
        "Session Info"
      ],
      "created": "2019-05-31 12:56:32",
      "modified": "2019-08-05 10:56:04",
      "commits": 8
    }
  ],
  "_score": 8.527578349505394,
  "_indexed": true,
  "_nocasepkg": "proda",
  "_universes": [
    "bioc",
    "const-ae"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-09-17T10:08:40.000Z",
      "distro": "resolute",
      "commit": "ae2d3b17498a68ebd3a5a29e4e5afa4bd2883134",
      "fileid": "https://r2.ropensci.org/98fe888459d9fb78ba5280879531fb87aee78017ef58d405c1e14b187f1adfcd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35207999802"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-09-17T10:09:11.000Z",
      "distro": "resolute",
      "commit": "ae2d3b17498a68ebd3a5a29e4e5afa4bd2883134",
      "fileid": "https://r2.ropensci.org/7c2516056a7d8e7767028a64ed0ae35018821296c6925c2dff482919dd3bf196",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35207999802"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-09-17T11:19:45.000Z",
      "commit": "ae2d3b17498a68ebd3a5a29e4e5afa4bd2883134",
      "fileid": "https://r2.ropensci.org/54005caa7d3ef246009ed72e73bd2bec7af6e317c8509d2ff69ebfb9016bc098",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35207999802"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-09-17T11:20:00.000Z",
      "commit": "ae2d3b17498a68ebd3a5a29e4e5afa4bd2883134",
      "fileid": "https://r2.ropensci.org/7e61123f799982cdf827fcc1953b81580f9dd0a261e5b34577aac283eb08c7c9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35207999802"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.27.0",
      "date": "2026-09-17T10:07:52.000Z",
      "commit": "ae2d3b17498a68ebd3a5a29e4e5afa4bd2883134",
      "fileid": "https://r2.ropensci.org/744f3d80e5330f48697e0c55c09eedac24551bddc521c6d277a645389d10cdca",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35207999802"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-09-17T10:06:25.000Z",
      "commit": "ae2d3b17498a68ebd3a5a29e4e5afa4bd2883134",
      "fileid": "https://r2.ropensci.org/7683d6c3f09714f40f4a2658bb320a107400104d92872b5fbfada3041bd1cfb8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35207999802"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-09-17T10:06:50.000Z",
      "commit": "ae2d3b17498a68ebd3a5a29e4e5afa4bd2883134",
      "fileid": "https://r2.ropensci.org/39e51748d3d4888ed8a6fe03f28c596404f6c6bbd0c6d909133a6247fd0458f7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35207999802"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-09-17T10:06:43.000Z",
      "commit": "ae2d3b17498a68ebd3a5a29e4e5afa4bd2883134",
      "fileid": "https://r2.ropensci.org/c0b9a4eccb16612633a5592f52ff59ad2c36f1dff92284549a1c51591a722cc1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35207999802"
    }
  ]
}