{
  "_id": "6aabc7733d719c1f8406e988",
  "Package": "beer",
  "Type": "Package",
  "Title": "Bayesian Enrichment Estimation in R",
  "Version": "1.17.0",
  "Authors@R": "c(person(\"Athena\", \"Chen\", email = \"achen70@jhu.edu\", \nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-6900-2264\")),\nperson(\"Rob\", \"Scharpf\", email = \"rscharpf@jhu.edu\",\nrole = c(\"aut\")),\nperson(\"Ingo\", \"Ruczinski\", email = \"ingo@jhu.edu\",\nrole = c(\"aut\")))",
  "Description": "BEER implements a Bayesian model for analyzing\nphage-immunoprecipitation sequencing (PhIP-seq) data. Given a\nPhIPData object, BEER returns posterior probabilities of\nenriched antibody responses, point estimates for the relative\nfold-change in comparison to negative control samples, and\nmore. Additionally, BEER provides a convenient implementation\nfor using edgeR to identify enriched antibody responses.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "SystemRequirements": "JAGS (4.3.0)",
  "biocViews": "Software, StatisticalMethod, Bayesian, Sequencing, Coverage",
  "URL": "https://github.com/athchen/beer/",
  "BugReports": "https://github.com/athchen/beer/issues",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "Language": "en-US",
  "Config/pak/sysreqs": "jags libicu-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:57:48 UTC",
  "RemoteUrl": "https://github.com/bioc/beer",
  "RemoteRef": "HEAD",
  "RemoteSha": "2ad6b135eabab8a38489c561d001a7d0e5f6c14f",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-17 09:48:50 UTC",
    "User": "root"
  },
  "Author": "Athena Chen [aut, cre] (ORCID: <https://orcid.org/0000-0001-6900-2264>),\nRob Scharpf [aut],\nIngo Ruczinski [aut]",
  "Maintainer": "Athena Chen <achen70@jhu.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "beer_1.17.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/350e0b6302cf92f85bae0bb39409b00ef7b7bc411fd500c638f3876b6f4fa730",
  "_filesize": 867252,
  "_sha256": "350e0b6302cf92f85bae0bb39409b00ef7b7bc411fd500c638f3876b6f4fa730",
  "_expires": "2026-12-26T10:56:48.000Z",
  "_created": "2026-09-17T09:48:50.000Z",
  "_published": "2026-09-17T10:56:50.929Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 5
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35206660256",
  "_status": "success",
  "_upstream": "https://github.com/bioc/beer",
  "_commit": {
    "id": "2ad6b135eabab8a38489c561d001a7d0e5f6c14f",
    "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": 1777381068
  },
  "_maintainer": {
    "name": "Athena Chen",
    "email": "achen70@jhu.edu",
    "login": "athchen",
    "description": "data scientist and statistician at Gate Biosciences. Recent PhD graduate from the department of biostatistics at Johns Hopkins SPH",
    "uuid": 10517467,
    "orcid": "0000-0001-6900-2264"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 105155826543,
      "time": 192,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10490423188"
    },
    {
      "job": 105155826540,
      "time": 549,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "10490906575"
    },
    {
      "job": 105155826538,
      "time": 538,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "10491115588"
    },
    {
      "job": 105155826522,
      "time": 330,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "10493836259"
    },
    {
      "job": 105155826591,
      "time": 290,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "10494520957"
    },
    {
      "job": 105154106617,
      "time": 347,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10489689302"
    },
    {
      "job": 105155826688,
      "time": 143,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10490368444"
    },
    {
      "job": 105155826557,
      "time": 911,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "10491036394"
    },
    {
      "job": 105155826565,
      "time": 964,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "10491246270"
    },
    {
      "job": 105155826762,
      "time": 898,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "10490596888"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "PhIPData",
      "version": ">= 1.1.1",
      "role": "Depends"
    },
    {
      "package": "rjags",
      "role": "Depends"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "progressr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "codetools",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-45",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.17.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.15.1",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "statisticalmethod",
    "bayesian",
    "sequencing",
    "coverage",
    "jags",
    "cpp"
  ],
  "_stars": 11,
  "_contributors": [
    {
      "user": "athchen",
      "count": 67,
      "uuid": 10517467
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 2,
      "uuid": 2746443
    },
    {
      "user": "lshep",
      "count": 1,
      "uuid": 18724380
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 467,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 402,
    "source": "https://www.bioconductor.org/packages/stats/bioc/beer"
  },
  "_devurl": "https://github.com/athchen/beer",
  "_searchresults": 18,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/beer.html",
    "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/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/athchen/beer",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "beadsRR",
    "brew",
    "brewOne",
    "edgeROne",
    "edgeROneQLF",
    "getAB",
    "getBF",
    "getExpected",
    "guessEnriched",
    "runEdgeR"
  ],
  "_help": [
    {
      "page": "dot-beadsRRBeer",
      "title": "Function to run the beads-only round robin using BEER",
      "topics": [
        ".beadsRRBeer"
      ]
    },
    {
      "page": "dot-beadsRREdgeR",
      "title": "Function to run the beads-only round robin using edgeR",
      "topics": [
        ".beadsRREdgeR"
      ]
    },
    {
      "page": "dot-brewSamples",
      "title": "Run BEER for all samples",
      "topics": [
        ".brewSamples"
      ]
    },
    {
      "page": "dot-checkCounts",
      "title": "Function to check that the counts matrix only contains integers",
      "topics": [
        ".checkCounts"
      ]
    },
    {
      "page": "dot-checkOverwrite",
      "title": "Function to check whether an assay will be overwritten",
      "topics": [
        ".checkOverwrite"
      ]
    },
    {
      "page": "dot-edgeRBeads",
      "title": "Estimate edgeR dispersion parameters from the beads-only data using qCML",
      "topics": [
        ".edgeRBeads"
      ]
    },
    {
      "page": "dot-edgeRBeadsQLF",
      "title": "Estimate edgeR dispersion parameters from the beads-only samples using Cox-Reid profile adjusted likelihood method for estimating dispersions.",
      "topics": [
        ".edgeRBeadsQLF"
      ]
    },
    {
      "page": "dot-getABEdgeR",
      "title": "Derive beta shape parameters using edgeR dispersion estimates",
      "topics": [
        ".getABEdgeR"
      ]
    },
    {
      "page": "dot-getABMLE",
      "title": "Wrapper function to derive MLE estimates of a, b from beads-only samples",
      "topics": [
        ".getABMLE"
      ]
    },
    {
      "page": "dot-getABMLEProp",
      "title": "Helper function to derive MLE estimates of a, b from a vector of proportions",
      "topics": [
        ".getABMLEProp"
      ]
    },
    {
      "page": "dot-getABMOM",
      "title": "Wrapper function to derive MOM estimates of a, b from beads-only samples",
      "topics": [
        ".getABMOM"
      ]
    },
    {
      "page": "dot-getABMOMProp",
      "title": "Helper function to derive MOM estimates of a, b from a vector of proportions",
      "topics": [
        ".getABMOMProp"
      ]
    },
    {
      "page": "dot-guessEnrichedEdgeR",
      "title": "Guess super-enriched peptides based on edgeR fold-change estimates",
      "topics": [
        ".guessEnrichedEdgeR"
      ]
    },
    {
      "page": "dot-guessEnrichedMLE",
      "title": "Guess enriched peptides based on MLE estimates of the true fold-change",
      "topics": [
        ".guessEnrichedMLE"
      ]
    },
    {
      "page": "dot-tidyAssayNames",
      "title": "Clean-up specified assay names",
      "topics": [
        ".tidyAssayNames"
      ]
    },
    {
      "page": "dot-tidyInputsJAGS",
      "title": "Clean inputs for JAGS parameters",
      "topics": [
        ".tidyInputsJAGS"
      ]
    },
    {
      "page": "dot-tidyInputsPrior",
      "title": "Clean up inputs for prior estimation",
      "topics": [
        ".tidyInputsPrior"
      ]
    },
    {
      "page": "dot-tidyInputsSE",
      "title": "Clean up inputs for identifying super-enriched peptides",
      "topics": [
        ".tidyInputsSE"
      ]
    },
    {
      "page": "beadsRR",
      "title": "Beads-only round robin",
      "topics": [
        "beadsRR"
      ]
    },
    {
      "page": "brew",
      "title": "Bayesian Enrichment Estimation in R (BEER)",
      "topics": [
        "brew"
      ]
    },
    {
      "page": "brewOne",
      "title": "Run BEER for one sample",
      "topics": [
        "brewOne"
      ]
    },
    {
      "page": "edgeROne",
      "title": "Run edgeR for one sample against all the beads-only samples.",
      "topics": [
        "edgeROne"
      ]
    },
    {
      "page": "edgeROneQLF",
      "title": "Run edgeR for one sample against all the beads-only samples using edgeR's QLF Test for differential expression.",
      "topics": [
        "edgeROneQLF"
      ]
    },
    {
      "page": "getAB",
      "title": "Estimate beads-only shape parameters",
      "topics": [
        "getAB"
      ]
    },
    {
      "page": "getBF",
      "title": "Calculate Bayes Factors",
      "topics": [
        "getBF"
      ]
    },
    {
      "page": "getExpected",
      "title": "Calculate expected read counts or proportion of reads",
      "topics": [
        "getExpected"
      ]
    },
    {
      "page": "guessEnriched",
      "title": "Identifying clearly enriched peptides",
      "topics": [
        "guessEnriched"
      ]
    },
    {
      "page": "guessInits",
      "title": "Derive initial estimates of unknown model parameters",
      "topics": [
        "guessInits"
      ]
    },
    {
      "page": "runEdgeR",
      "title": "Run edgeR on PhIP-Seq data",
      "topics": [
        "runEdgeR"
      ]
    },
    {
      "page": "summarizeRun",
      "title": "Summarize MCMC chain and return point estimates for BEER parameters",
      "topics": [
        "summarizeRun"
      ]
    },
    {
      "page": "summarizeRunOne",
      "title": "Derive point estimates for c, pi, phi, and Z for a particular sample",
      "topics": [
        "summarizeRunOne"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/beer/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/beer/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "BiocParallel",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "coda",
    "codetools",
    "cpp11",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "dplyr",
    "edgeR",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "httr2",
    "IRanges",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "openssl",
    "PhIPData",
    "pillar",
    "pkgconfig",
    "progressr",
    "purrr",
    "R6",
    "rjags",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libjags",
      "package": "jags",
      "headers": "jags",
      "source": "jags",
      "version": "4.3.2-2.2604.0",
      "name": "jags",
      "homepage": "https://mcmc-jags.sourceforge.io",
      "description": "Just Another Gibbs Sampler for Bayesian MCMC - binary"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "beer.Rmd",
      "filename": "beer.html",
      "title": "Estimating Enrichment in PhIP-Seq Experiments with BEER",
      "author": "Athena Chen, Kai Kammers, Rob Scharpf, Ingo Ruczinski",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "rjags",
        "beer",
        "Simulated data",
        "edgeR",
        "BEER (Bayesian Estimation Enrichment in R)",
        "Prior parameters",
        "Removing super enriched peptides",
        "Saving MCMC samples",
        "Visualizing MCMC Convergence",
        "Beads-only round robin",
        "Parallelization",
        "Plot Helpers",
        "getExpected()",
        "getBF()",
        "sessionInfo()"
      ],
      "created": "2021-02-23 00:40:57",
      "modified": "2022-06-30 23:21:45",
      "commits": 14
    }
  ],
  "_score": 5.7737864449811935,
  "_indexed": true,
  "_nocasepkg": "beer",
  "_universes": [
    "bioc",
    "athchen"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.17.0",
      "date": "2026-09-17T09:53:26.000Z",
      "distro": "resolute",
      "commit": "2ad6b135eabab8a38489c561d001a7d0e5f6c14f",
      "fileid": "https://r2.ropensci.org/edb0280241ce08882bbb5c8fa180661186c2351eb610b8bf33487a84cc367470",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35206660256"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.17.0",
      "date": "2026-09-17T09:53:14.000Z",
      "distro": "resolute",
      "commit": "2ad6b135eabab8a38489c561d001a7d0e5f6c14f",
      "fileid": "https://r2.ropensci.org/07410803f387db8f9c6db90bc7afcf78262956f7b90db21362750eb6faa7733f",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35206660256"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.17.0",
      "date": "2026-09-17T10:52:40.000Z",
      "commit": "2ad6b135eabab8a38489c561d001a7d0e5f6c14f",
      "fileid": "https://r2.ropensci.org/08032d5178dbabb457df0ed95405e971928c719a76eda2a4bf8d001c267dadab",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35206660256"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.17.0",
      "date": "2026-09-17T10:53:08.000Z",
      "commit": "2ad6b135eabab8a38489c561d001a7d0e5f6c14f",
      "fileid": "https://r2.ropensci.org/92fd4434bee4e8e19e2139c3bc752a62a142cc329a9bd9f7392b6cbfdc0722e0",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35206660256"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.17.0",
      "date": "2026-09-17T09:51:49.000Z",
      "commit": "2ad6b135eabab8a38489c561d001a7d0e5f6c14f",
      "fileid": "https://r2.ropensci.org/ac6e2285d0b71563aaf6992a3a17056ffdff349c8dc52d6f7f9cfb2e0b549b7d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35206660256"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-09-17T09:51:06.000Z",
      "commit": "2ad6b135eabab8a38489c561d001a7d0e5f6c14f",
      "fileid": "https://r2.ropensci.org/ab9a2f5628258342e2686c4df1820dc6c4b5d7a9954eb8c08d838294db2d2eeb",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35206660256"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-09-17T09:50:45.000Z",
      "commit": "2ad6b135eabab8a38489c561d001a7d0e5f6c14f",
      "fileid": "https://r2.ropensci.org/4ba26c1ffe4486b23cf93909a88c8ac9bacae9a40c66d3efa4c85c047aa1c267",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35206660256"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-09-17T09:50:55.000Z",
      "commit": "2ad6b135eabab8a38489c561d001a7d0e5f6c14f",
      "fileid": "https://r2.ropensci.org/493318d1a98b0a78bf505bbd121b1a2869458e7e71968a9a67ef92b1f0f4190b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35206660256"
    }
  ]
}