{ "_id": "6a4976496d67900babdf57d9", "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": "2026-06-23 15:41:37 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "GENIE3_1.35.0.tar.gz", "_fileid": "https://r2.ropensci.org/07ed2397c215a1672871394533fcfcf878ab49b8e3bf8af293a033f8cfd485a6", "_filesize": 121258, "_sha256": "07ed2397c215a1672871394533fcfcf878ab49b8e3bf8af293a033f8cfd485a6", "_expires": "2026-10-12T21:08:23.000Z", "_created": "2026-06-23T15:41:37.000Z", "_published": "2026-07-04T21:08:25.383Z", "_bioccheck": { "error": 1, "warning": 2, "note": 10 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289", "_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": 85167128388, "time": 168, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7825850352" }, { "job": 85167128399, "time": 172, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7825853499" }, { "job": 85167128466, "time": 223, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7825874601" }, { "job": 85167128440, "time": 152, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7825845525" }, { "job": 85167128400, "time": 211, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7825869494" }, { "job": 85167128484, "time": 115, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7826048183" }, { "job": 85167128502, "time": 229, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7826096952" }, { "job": 85167128395, "time": 89, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7826032563" }, { "job": 85167128347, "time": 257, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7826104803" }, { "job": 85167128351, "time": 193, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7825775006" }, { "job": 85167128431, "time": 227, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7825876715" }, { "job": 85167128300, "time": 101, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7825821016" }, { "job": 85167128508, "time": 83, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7825813415" }, { "job": 85167128331, "time": 108, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7825824288" } ], "_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": 441, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 172, "_searchresults": 235, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GENIE3.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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": 7.450249108319362, "_indexed": true, "_nocasepkg": "genie3", "_universes": [ "bioc", "vahuynh" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-06-23T15:44:28.000Z", "distro": "resolute", "arch": "aarch64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/e37c1727057d00dccbf7810fe9102ebf6d4680072c138112032f8a6248cf751a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" }, { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-06-23T15:45:10.000Z", "distro": "resolute", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/3f9ce49310fdce57b4ce5a90e0795aca0928aaa41a49e0386bb4e80f42b52b15", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" }, { "r": "4.6.0", "os": "linux", "version": "1.35.0", "date": "2026-06-23T15:44:09.000Z", "distro": "resolute", "arch": "aarch64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/6f0bb9cdcfe2ffc13f34ebc3bdacecb37157ab4fe5c00d538b39543c420512af", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" }, { "r": "4.6.0", "os": "linux", "version": "1.35.0", "date": "2026-06-23T15:44:58.000Z", "distro": "resolute", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/9d6c7d217945035e38f67d5f718eded754f5dd479470807b04dd0786d3284d8a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-06-23T15:51:58.000Z", "arch": "aarch64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/3bc17b2f05c2262a7a4bd491225c5b0e18f49d1631038edf09a4841fa2aec7fb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-06-23T15:53:01.000Z", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/2188722047857d86c5013f2c854a0934501ac4f623c7f4563bb52065cc8ce453", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" }, { "r": "4.6.0", "os": "mac", "version": "1.35.0", "date": "2026-06-23T15:51:23.000Z", "arch": "aarch64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/239445b569676c7ea12c4d359047d63cd87f49c31a1f7567383c6dbae78b0286", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" }, { "r": "4.6.0", "os": "mac", "version": "1.35.0", "date": "2026-06-23T15:53:23.000Z", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/f6c5b084fd89345b4de9411b6a92bad15ba43ff9f5a5c77b8e9f9c79dca39f1e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" }, { "r": "4.6.0", "os": "wasm", "version": "1.35.0", "date": "2026-06-23T15:45:41.000Z", "arch": "emscripten", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/bba663287bd10b39abe687f629500d6050885d14fc26d46fe86000c611995253", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" }, { "r": "4.7.0", "os": "win", "version": "1.35.0", "date": "2026-06-23T15:42:58.000Z", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/dfae13e5911c524132ec04054cdc8b13dd48e5d88c2ad1aa46a0ba5890e53e64", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" }, { "r": "4.5.3", "os": "win", "version": "1.35.0", "date": "2026-06-23T15:42:45.000Z", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/b6d86f72e2a9daa885bdf92fe94a7d61c2e0f028c7174e4892c53c7a12ee4150", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" }, { "r": "4.6.0", "os": "win", "version": "1.35.0", "date": "2026-06-23T15:42:59.000Z", "arch": "x86_64", "commit": "0146353a24f75dec93ef89fcccb6bdb36cd9dbf9", "fileid": "https://r2.ropensci.org/08f8489f612f669f014cbdafcf34ef1ab6b3fd4de44c438fe8103231b61ab5bd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037656289" } ] }