{
  "_id": "6ae5c83b327abcdf8686a08b",
  "Package": "biotmle",
  "Title": "Targeted Learning with Moderated Statistics for Biomarker\nDiscovery",
  "Version": "1.37.1",
  "Authors@R": "c(\nperson(\"Nima\", \"Hejazi\", email = \"nh@nimahejazi.org\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-7127-2789\")),\nperson(\"Alan\", \"Hubbard\", email = \"hubbard@berkeley.edu\",\nrole = c(\"aut\", \"ths\"),\ncomment = c(ORCID = \"0000-0002-3769-0127\")),\nperson(\"Mark\", \"van der Laan\", email = \"laan@stat.berkeley.edu\",\nrole = c(\"aut\", \"ths\"),\ncomment = c(ORCID = \"0000-0003-1432-5511\")),\nperson(\"Weixin\", \"Cai\", email = \"wcai@berkeley.edu\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-2680-3066\")),\nperson(\"Philippe\", \"Boileau\", email = \"philippe_boileau@berkeley.edu\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4850-2507\"))\n)",
  "Description": "Tools for differential expression biomarker discovery\nbased on microarray and next-generation sequencing data that\nleverage efficient semiparametric estimators of the average\ntreatment effect for variable importance analysis. Estimation\nand inference of the (marginal) average treatment effects of\npotential biomarkers are computed by targeted minimum\nloss-based estimation, with joint, stable inference constructed\nacross all biomarkers using a generalization of moderated\nstatistics for use with the estimated efficient influence\nfunction. The procedure accommodates the use of ensemble\nmachine learning for the estimation of nuisance functions.",
  "License": "MIT + file LICENSE",
  "URL": "https://code.nimahejazi.org/biotmle",
  "BugReports": "https://github.com/nhejazi/biotmle/issues",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "biocViews": "Regression, GeneExpression, DifferentialExpression,\nSequencing, Microarray, RNASeq, ImmunoOncology",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-07-27 18:05:30 UTC",
  "RemoteUrl": "https://github.com/bioc/biotmle",
  "RemoteRef": "HEAD",
  "RemoteSha": "e86a3da16d1cbd076c0f1aac44b412044f9601c2",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-31 10:13:25 UTC",
    "User": "root"
  },
  "Author": "Nima Hejazi [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0002-7127-2789>),\nAlan Hubbard [aut, ths] (ORCID:\n<https://orcid.org/0000-0002-3769-0127>),\nMark van der Laan [aut, ths] (ORCID:\n<https://orcid.org/0000-0003-1432-5511>),\nWeixin Cai [ctb] (ORCID: <https://orcid.org/0000-0003-2680-3066>),\nPhilippe Boileau [ctb] (ORCID: <https://orcid.org/0000-0002-4850-2507>)",
  "Maintainer": "Nima Hejazi <nh@nimahejazi.org>",
  "_user": "bioc",
  "_type": "src",
  "_file": "biotmle_1.37.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/72fafec8eb649b109bf13aab2ce11571b6d974273b401cef39681ecd6f9d40d7",
  "_filesize": 271816,
  "_sha256": "72fafec8eb649b109bf13aab2ce11571b6d974273b401cef39681ecd6f9d40d7",
  "_expires": "2027-02-08T10:51:37.000Z",
  "_created": "2026-10-31T10:13:25.000Z",
  "_published": "2026-10-31T10:51:39.042Z",
  "_upstream": "https://github.com/bioc/biotmle",
  "_status": "success",
  "_maintainer": {
    "name": "Nima Hejazi",
    "email": "nh@nimahejazi.org",
    "login": "nhejazi",
    "bluesky": "@nimahejazi.org",
    "linkedin": "in/nshejazi",
    "orcid": "0000-0002-7127-2789",
    "description": "assistant professor of biostatistics at the harvard school of public health working on causal {inference, machine learning}",
    "uuid": 8527276
  },
  "_jobs": [
    {
      "job": 124510242165,
      "time": 171,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "13039425755"
    },
    {
      "job": 124510242193,
      "time": 344,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13039690862"
    },
    {
      "job": 124510242161,
      "time": 405,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13039690978"
    },
    {
      "job": 124510242148,
      "time": 264,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13039734545"
    },
    {
      "job": 124510242163,
      "time": 278,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13039774394"
    },
    {
      "job": 124509339586,
      "time": 263,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13039365796"
    },
    {
      "job": 124510242158,
      "time": 140,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13039645552"
    },
    {
      "job": 124510242220,
      "time": 269,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13038789963"
    },
    {
      "job": 124510242195,
      "time": 231,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13039236466"
    },
    {
      "job": 124510242191,
      "time": 276,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13039181540"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 4
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41191447543",
  "_commit": {
    "id": "e86a3da16d1cbd076c0f1aac44b412044f9601c2",
    "author": "nima hejazi <nh@nimahejazi.org>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #80 from nhejazi/drop-superheat\n\nreplace superheat with ggplot",
    "time": 1785175530
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggsci",
      "role": "Imports"
    },
    {
      "package": "ggdendro",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "assertthat",
      "role": "Imports"
    },
    {
      "package": "drtmle",
      "version": ">= 1.0.4",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "arm",
      "role": "Suggests"
    },
    {
      "package": "earth",
      "role": "Suggests"
    },
    {
      "package": "ranger",
      "role": "Suggests"
    },
    {
      "package": "SuperLearner",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "DBI",
      "role": "Suggests"
    },
    {
      "package": "biotmleData",
      "version": ">= 1.1.1",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-30",
      "n": 1
    },
    {
      "week": "2026-31",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.37.1",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.36.1",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "regression",
    "geneexpression",
    "differentialexpression",
    "sequencing",
    "microarray",
    "rnaseq",
    "immunooncology",
    "bioconductor",
    "bioconductor-package",
    "bioconductor-packages",
    "bioinformatics",
    "biomarker-discovery",
    "biostatistics",
    "causal-inference",
    "computational-biology",
    "machine-learning",
    "statistics",
    "targeted-learning"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "nhejazi",
      "count": 329,
      "uuid": 8527276
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "philboileau",
      "count": 2,
      "uuid": 8812813
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 480,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 617,
    "source": "https://www.bioconductor.org/packages/stats/bioc/biotmle"
  },
  "_devurl": "https://github.com/nhejazi/biotmle",
  "_searchresults": 12,
  "_abi": {
    "exports": [
      {
        "key": "biotmle::bioTMLE",
        "hash": "eedf9b76bad0b682"
      },
      {
        "key": "biotmle::data.frame_OR_EList",
        "hash": "6e9850dc63f861f8"
      }
    ],
    "imports": [
      {
        "key": "S4Vectors::Annotated",
        "hash": "9b5b8ee6ad9969f8"
      },
      {
        "key": "S4Vectors::RectangularData",
        "hash": "d414a10823a4aada"
      },
      {
        "key": "S4Vectors::Vector",
        "hash": "09cab0bd77ae353b"
      },
      {
        "key": "S4Vectors::vector_OR_Vector",
        "hash": "f3fc18c9f8ff2633"
      },
      {
        "key": "SummarizedExperiment::SummarizedExperiment",
        "hash": "d53ca73257d1e8cf"
      }
    ]
  },
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/biotmle.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/nhejazi/biotmle",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    ".biotmle",
    "biomarkertmle",
    "eif",
    "heatmap_ic",
    "modtest_ic",
    "rnaseq_ic",
    "toptable",
    "volcano_ic"
  ],
  "_help": [
    {
      "page": "biomarkertmle",
      "title": "Biomarker Evaluation with Targeted Minimum Loss Estimation of the ATE",
      "topics": [
        "biomarkertmle"
      ]
    },
    {
      "page": "bioTMLE-class",
      "title": "Constructor for class bioTMLE",
      "topics": [
        ".biotmle",
        "bioTMLE-class"
      ]
    },
    {
      "page": "data.frame_OR_EList-class",
      "title": "S4 class union data.frame_OR_EList",
      "topics": [
        "data.frame_OR_EList-class"
      ]
    },
    {
      "page": "eif",
      "title": "Accessor for Table of Raw Efficient Influence Function Values",
      "topics": [
        "eif"
      ]
    },
    {
      "page": "exp_biomarkertmle",
      "title": "TMLE procedure using ATE for Biomarker Identication from Exposure",
      "topics": [
        "exp_biomarkertmle"
      ]
    },
    {
      "page": "heatmap_ic",
      "title": "Heatmap for class biotmle",
      "topics": [
        "heatmap_ic"
      ]
    },
    {
      "page": "modtest_ic",
      "title": "Moderated Statistical Tests for Influence Functions",
      "topics": [
        "modtest_ic"
      ]
    },
    {
      "page": "plot.bioTMLE",
      "title": "Plot p-values from moderated statistical tests for class biotmle",
      "topics": [
        "plot.bioTMLE"
      ]
    },
    {
      "page": "rnaseq_ic",
      "title": "Utility for using voom transformation with TMLE for biomarker discovery",
      "topics": [
        "rnaseq_ic"
      ]
    },
    {
      "page": "toptable",
      "title": "Accessor for Results of Moderated Influence Function Hypothesis Testing",
      "topics": [
        "toptable"
      ]
    },
    {
      "page": "volcano_ic",
      "title": "Volcano plot for class biotmle",
      "topics": [
        "volcano_ic"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/biotmle/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "assertthat",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "bitops",
    "boot",
    "caTools",
    "cli",
    "codetools",
    "cpp11",
    "crs",
    "cvAUC",
    "data.table",
    "DelayedArray",
    "digest",
    "dplyr",
    "drtmle",
    "farver",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "future",
    "future.apply",
    "gam",
    "generics",
    "GenomicRanges",
    "ggdendro",
    "ggplot2",
    "ggsci",
    "globals",
    "glue",
    "gplots",
    "gtable",
    "gtools",
    "IRanges",
    "isoband",
    "iterators",
    "KernSmooth",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "listenv",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "nnls",
    "np",
    "parallelly",
    "patchwork",
    "pillar",
    "pkgconfig",
    "quadprog",
    "quantreg",
    "R6",
    "RColorBrewer",
    "rlang",
    "ROCR",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SparseM",
    "statmod",
    "SummarizedExperiment",
    "SuperLearner",
    "survival",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "exposureBiomarkers.Rmd",
      "filename": "exposureBiomarkers.html",
      "title": "Identifying Biomarkers from an Exposure Variable with biotmle",
      "author": "Nima Hejazi",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Biomarker Identification",
        "Visualization of Results",
        "Session Information"
      ],
      "created": "2017-01-17 17:04:43",
      "modified": "2026-07-27 18:05:30",
      "commits": 29
    }
  ],
  "_score": 5.477121254719663,
  "_indexed": true,
  "_nocasepkg": "biotmle",
  "_universes": [
    "bioc",
    "nhejazi"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.37.1",
      "date": "2026-10-31T10:17:29.000Z",
      "distro": "resolute",
      "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2",
      "fileid": "https://r2.ropensci.org/568dfbb5540c3a6def7bc098e608fbf59ff3f62eb05dcf1c6fc5f01b189b0d92",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41191447543"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.37.1",
      "date": "2026-10-31T10:17:41.000Z",
      "distro": "resolute",
      "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2",
      "fileid": "https://r2.ropensci.org/2ae04a0d940aaf9e235997cb432280acc73123d8fb7a56b0ee6d1d11394d3dc9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41191447543"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.37.1",
      "date": "2026-10-31T10:48:37.000Z",
      "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2",
      "fileid": "https://r2.ropensci.org/b4e5ba87c3650e7be864e3381ca6b078e1892c56ab6eca8c76eba07ae23741c4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41191447543"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.37.1",
      "date": "2026-10-31T10:48:32.000Z",
      "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2",
      "fileid": "https://r2.ropensci.org/684a99bfc7196fb3afb80213a9a33288ff3b76820155cf9ff5918f17c5577acf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41191447543"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.37.1",
      "date": "2026-10-31T10:16:13.000Z",
      "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2",
      "fileid": "https://r2.ropensci.org/93cec491bf600c68140c86c1de3a86bd73ca19737b505d917ca389ea4a436102",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41191447543"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.37.1",
      "date": "2026-10-31T10:15:23.000Z",
      "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2",
      "fileid": "https://r2.ropensci.org/b50d93734d66aad3715150024ed8225bb84f9258e092c3b659ca343d7b1f3709",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41191447543"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.37.1",
      "date": "2026-10-31T10:15:13.000Z",
      "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2",
      "fileid": "https://r2.ropensci.org/21227d725d3265c78d14a8831213020cb029c7ff290c9c40627d786b6ee5140f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41191447543"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.37.1",
      "date": "2026-10-31T10:15:32.000Z",
      "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2",
      "fileid": "https://r2.ropensci.org/208492aa26df2042a8ad8adc1ba013f7e22bd7c69be98bba0c446fb75271bca0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41191447543"
    }
  ]
}