{ "_id": "6ac9ea59fe5cc25786e82a0f", "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": "make zlib1g-dev", "Repository": "https://nhejazi.r-universe.dev", "Date/Publication": "2026-07-27 18:05:30 UTC", "RemoteUrl": "https://github.com/nhejazi/biotmle", "RemoteRef": "HEAD", "RemoteSha": "e86a3da16d1cbd076c0f1aac44b412044f9601c2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-08 11:33:42 UTC", "User": "root" }, "Author": "Nima Hejazi [aut, cre, cph] (ORCID:\n),\nAlan Hubbard [aut, ths] (ORCID:\n),\nMark van der Laan [aut, ths] (ORCID:\n),\nWeixin Cai [ctb] (ORCID: ),\nPhilippe Boileau [ctb] (ORCID: )", "Maintainer": "Nima Hejazi ", "_user": "nhejazi", "_type": "src", "_file": "biotmle_1.37.1.tar.gz", "_fileid": "https://r2.ropensci.org/9e86feae0f10e6452e6a384006fb2b37b885286636f0015c7f55d352fe8b2cd0", "_filesize": 272418, "_sha256": "9e86feae0f10e6452e6a384006fb2b37b885286636f0015c7f55d352fe8b2cd0", "_expires": "2027-01-16T12:03:47.000Z", "_created": "2026-10-08T11:33:42.000Z", "_published": "2026-10-10T07:33:45.596Z", "_buildurl": "https://github.com/r-universe/nhejazi/actions/runs/37770377311", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 114162181645, "time": 302, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11548071774" }, { "job": 114162181343, "time": 298, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11547507068" }, { "job": 114162180647, "time": 93, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 114162181302, "time": 398, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11549375909" }, { "job": 114162181433, "time": 249, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11547835960" }, { "job": 114162181643, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11547936444" }, { "job": 114162181428, "time": 300, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11548720702" }, { "job": 114162180772, "time": 106, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 114162181636, "time": 267, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11548610883" } ], "_upstream": "https://github.com/nhejazi/biotmle", "_commit": { "id": "e86a3da16d1cbd076c0f1aac44b412044f9601c2", "author": "nima hejazi ", "committer": "GitHub ", "message": "Merge pull request #80 from nhejazi/drop-superheat\n\nreplace superheat with ggplot", "time": 1785175530 }, "_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 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.6.0", "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": "nhejazi", "_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": 8527276, "type": "user", "name": "nima hejazi", "followers": 233, "description": "assistant professor of biostatistics at the harvard school of public health working on causal {inference, machine learning}" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/biotmle" }, "_devurl": "https://github.com/nhejazi/biotmle", "_searchresults": 5, "_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": true, "_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/nhejazi/biotmle/raw/HEAD/README.md", "_rundeps": [ "abind", "assertthat", "BH", "Biobase", "BiocGenerics", "BiocParallel", "bitops", "boot", "caTools", "cli", "codetools", "cpp11", "crs", "cubature", "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", "Rcpp", "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": 5.3979400086720375, "_indexed": false, "_nocasepkg": "biotmle", "_universes": [ "nhejazi" ], "_indexurl": "https://bioc.r-universe.dev/biotmle", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.37.1", "date": "2026-10-08T11:36:37.000Z", "distro": "resolute", "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2", "fileid": "https://r2.ropensci.org/76cda6ae84d7e7530cdf2d5d030fd1c1641ccf7c92a6fecbb4b3da2beff03b4b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nhejazi/actions/runs/37770377311" }, { "r": "4.6.1", "os": "linux", "version": "1.37.1", "date": "2026-10-08T11:36:35.000Z", "distro": "resolute", "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2", "fileid": "https://r2.ropensci.org/f9f68fc01115ff846f63eb6e2eab070bc8ffd9cf69ac9d5e51d61b118c489ea5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nhejazi/actions/runs/37770377311" }, { "r": "4.6.1", "os": "mac", "version": "1.37.1", "date": "2026-10-08T11:59:42.000Z", "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2", "fileid": "https://r2.ropensci.org/3f04744d4e03d3d153a9fb5ab163845ca07a41bca0898d359e2066b1a95842c8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nhejazi/actions/runs/37770377311" }, { "r": "4.6.0", "os": "wasm", "version": "1.37.1", "date": "2026-10-08T11:36:22.000Z", "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2", "fileid": "https://r2.ropensci.org/4af1f027feb508c0a7734f88b5bb1bc960aac7e4940cf908cce4d75e0a8ad010", "status": "success", "buildurl": "https://github.com/r-universe/nhejazi/actions/runs/37770377311" }, { "r": "4.7.0", "os": "win", "version": "1.37.1", "date": "2026-10-08T11:35:46.000Z", "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2", "fileid": "https://r2.ropensci.org/5a82d6cc26732414d26d3c867c8f33785b76c6616590beebe5ecdff68eff64ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nhejazi/actions/runs/37770377311" }, { "r": "4.6.1", "os": "win", "version": "1.37.1", "date": "2026-10-08T11:35:44.000Z", "commit": "e86a3da16d1cbd076c0f1aac44b412044f9601c2", "fileid": "https://r2.ropensci.org/5505a7e60b679e9dc4b28d87a0061d473cad1d59ae5c80d84c98916f07a2f0ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nhejazi/actions/runs/37770377311" } ] }