{ "_id": "6abb7efd99f7aa8c6aa44e2d", "Package": "GENIE3", "Type": "Package", "Title": "GEne Network Inference with Ensemble of trees", "Version": "1.35.0", "Date": "2022-04-05", "Author": "Van Anh Huynh-Thu, Sara Aibar, Pierre Geurts", "Maintainer": "Van Anh Huynh-Thu ", "Description": "This package implements the GENIE3 algorithm for inferring\ngene regulatory networks from expression data.", "License": "GPL (>= 2)", "NeedsCompilation": "yes", "RoxygenNote": "7.1.2", "VignetteBuilder": "knitr", "biocViews": "NetworkInference, SystemsBiology, DecisionTree, Regression,\nNetwork, GraphAndNetwork, GeneExpression", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:46:05 UTC", "RemoteUrl": "https://github.com/bioc/GENIE3", "RemoteRef": "HEAD", "RemoteSha": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "Packaged": { "Date": "2026-09-29 08:43:57 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "GENIE3_1.35.0.tar.gz", "_fileid": "https://r2.ropensci.org/d2494e5eef1e702a446b17221fec1c120649bdba5bd366613b96b052fdd8ad03", "_filesize": 120651, "_sha256": "d2494e5eef1e702a446b17221fec1c120649bdba5bd366613b96b052fdd8ad03", "_expires": "2027-01-07T09:03:55.000Z", "_created": "2026-09-29T08:43:57.000Z", "_published": "2026-09-29T09:03:56.900Z", "_bioccheck": { "error": 1, "warning": 3, "note": 10 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828", "_status": "success", "_upstream": "https://github.com/bioc/GENIE3", "_commit": { "id": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380365 }, "_maintainer": { "name": "Van Anh Huynh-Thu", "email": "vahuynh@uliege.be", "login": "vahuynh", "description": "Researcher in machine learning and bioinformatics", "uuid": 22789484 }, "_distro": "resolute", "_jobs": [ { "job": 109327922144, "time": 162, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11021464221" }, { "job": 109327922168, "time": 131, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "11021349158" }, { "job": 109327922137, "time": 227, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11022213121" }, { "job": 109327922038, "time": 130, "config": "linux-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11021532607" }, { "job": 109327922161, "time": 276, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11022455334" }, { "job": 109327922160, "time": 102, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11022652079" }, { "job": 109327922321, "time": 297, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11021644984" }, { "job": 109327922060, "time": 105, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11021674036" }, { "job": 109327922104, "time": 167, "config": "macos-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11022319502" }, { "job": 109326580465, "time": 229, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11021803242" }, { "job": 109327922062, "time": 122, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11022287004" }, { "job": 109327922250, "time": 281, "config": "windows-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "11021942690" }, { "job": 109327922389, "time": 183, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11021867459" }, { "job": 109327922190, "time": 93, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11021778505" }, { "job": 109327922192, "time": 211, "config": "windows-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11021669016" }, { "job": 109327922243, "time": 98, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11021608664" } ], "_registered": true, "_dependencies": [ { "package": "stats", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "foreach", "role": "Suggests" }, { "package": "doRNG", "role": "Suggests" }, { "package": "doParallel", "role": "Suggests" }, { "package": "Biobase", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "methods", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 4, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.35.0", "bioc": "3.24" }, { "branch": "release", "version": "1.34.0", "bioc": "3.23" } ], "_topics": [ "networkinference", "systemsbiology", "decisiontree", "regression", "network", "graphandnetwork", "geneexpression" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 470, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 2646, "source": "https://www.bioconductor.org/packages/stats/bioc/GENIE3" }, "_mentions": 172, "_searchresults": 4, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GENIE3.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "GENIE3", "getLinkList" ], "_help": [ { "page": "GENIE3", "title": "GENIE3", "topics": [ "GENIE3", "GENIE3,ExpressionSet-method", "GENIE3,matrix-method", "GENIE3,SummarizedExperiment-method" ] }, { "page": "getLinkList", "title": "getLinkList", "topics": [ "getLinkList" ] } ], "_readme": "https://github.com/bioc/GENIE3/raw/HEAD/README.md", "_rundeps": [ "cli", "dplyr", "generics", "glue", "lifecycle", "magrittr", "pillar", "pkgconfig", "plyr", "R6", "Rcpp", "reshape2", "rlang", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "GENIE3.Rmd", "filename": "GENIE3.html", "title": "GENIE3 vignette", "author": "Van Anh Huynh-Thu (vahuynh@uliege.be)", "engine": "knitr::rmarkdown", "headings": [ "Format of expression data", "Format of steady-state expression data", "How to run GENIE3", "Run GENIE3 with the default parameters", "Restrict the candidate regulators to a subset of genes", "Change the tree-based method and its settings", "Parallel GENIE3", "Obtain more information", "Get the list of the regulatory links", "Get all the regulatory links", "Get only the top-ranked links", "Get only the links with a weight higher than some threshold", "Important note on the interpretation of the weights" ], "created": "2016-11-04 16:06:06", "modified": "2023-08-16 09:20:29", "commits": 9 } ], "_score": 6.501771085899107, "_indexed": true, "_nocasepkg": "genie3", "_universes": [ "bioc", "vahuynh" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-09-29T08:46:08.000Z", "distro": "resolute", "arch": "aarch64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/1d0ee755c7b5c98255a662d063f723b71cbcb7c3778e0d26cb518b8cafdda48f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-09-29T08:47:25.000Z", "distro": "resolute", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/4736fac17e38338299344732dfa57c846d7670316c6f64b48dab5a438f782655", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.6.1", "os": "linux", "version": "1.35.0", "date": "2026-09-29T08:46:07.000Z", "distro": "resolute", "arch": "aarch64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/7ace44c773332a68ab14f69218de675caf332d2649e9ece7cff83871481b6c46", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.6.1", "os": "linux", "version": "1.35.0", "date": "2026-09-29T08:48:28.000Z", "distro": "resolute", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/bc5a45b34cb7447a4a109f8da9818f3779d5ff1ba2d400b278d02d500ccd1ee5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-09-29T09:02:06.000Z", "arch": "aarch64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/91bb11eb2a14ddc7fefb0503859d1f746730259367ed2e6a0e63aad83d72d89f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-09-29T09:02:14.000Z", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/27add8fe5b7100c06d9566f678a04c24667aa5931b7ce61298669696078698ec", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.6.1", "os": "mac", "version": "1.35.0", "date": "2026-09-29T08:57:01.000Z", "arch": "aarch64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/e03adc78ad612b6ccbe559e5c4d53048b88529f049af4e3837e12b3e5ac2a4f6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.6.1", "os": "mac", "version": "1.35.0", "date": "2026-09-29T09:00:26.000Z", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/7dc575ebb404e3a2e039d2707a4afb0b6c824338cb8f4ae8a67f0ace54aa4a5f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.6.0", "os": "wasm", "version": "1.35.0", "date": "2026-09-29T08:46:17.000Z", "arch": "emscripten", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/12e349738b4168ad49649b70e3f87840d4b1c57f8a0b1cf143b2b40cba2ee234", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.7.0", "os": "win", "version": "1.35.0", "date": "2026-09-29T08:48:23.000Z", "arch": "aarch64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/7dd13097c133ea5c42f2ef31202206acd13b6ae8fc57bd370064a969ae047975", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.7.0", "os": "win", "version": "1.35.0", "date": "2026-09-29T08:46:06.000Z", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/6bbf8b822f8d26b95cfef95ff6fcbabfbc4bd8c152871cef4b800a035dd955dc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.5.3", "os": "win", "version": "1.35.0", "date": "2026-09-29T08:45:14.000Z", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/8e376e1b82459f41cffb65ec1cb187292203caa8a0b4150c5137e0f3aff05d22", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.6.1", "os": "win", "version": "1.35.0", "date": "2026-09-29T08:47:15.000Z", "arch": "aarch64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/5380bfb3601f404fec7d07c1c46ef2b8745ac2fe925828b8dd1f90cb8f35fe3d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" }, { "r": "4.6.1", "os": "win", "version": "1.35.0", "date": "2026-09-29T08:45:16.000Z", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/c19dd9934e880b08c32d970dc797f71ae48aabbb64df7ef3da80ad8dafd85b3a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36544169828" } ] }