{ "_id": "6a1ace071d7bb097a09df8b2", "Package": "GRENITS", "Type": "Package", "Title": "Gene Regulatory Network Inference Using Time Series", "Version": "1.65.0", "Date": "2012-03-15", "Author": "Edward Morrissey", "Maintainer": "Edward Morrissey ", "Description": "The package offers four network inference statistical\nmodels using Dynamic Bayesian Networks and Gibbs Variable\nSelection: a linear interaction model, two linear interaction\nmodels with added experimental noise (Gaussian and Student\ndistributed) for the case where replicates are available and a\nnon-linear interaction model.", "License": "GPL (>= 2)", "LazyLoad": "yes", "biocViews": "NetworkInference, GeneRegulation, TimeCourse,\nGraphAndNetwork, GeneExpression, Network, Bayesian", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:35:35 UTC", "RemoteUrl": "https://github.com/bioc/GRENITS", "RemoteRef": "HEAD", "RemoteSha": "82b57b43aab244b2655712f30b0f8655c197061b", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 08:10:13 UTC", "User": "root" }, "MD5sum": "728cc463a691b4c8169c1b170f3c2a0a", "_user": "bioc", "_type": "src", "_file": "GRENITS_1.65.0.tar.gz", "_fileid": "42a20bb8b9dd16d18cf12173659d251d63f4c322ce868af27e656848441aae9f", "_filesize": 286818, "_sha256": "42a20bb8b9dd16d18cf12173659d251d63f4c322ce868af27e656848441aae9f", "_created": "2026-05-30T08:10:13.000Z", "_published": "2026-05-30T11:46:15.136Z", "_jobs": [ { "job": 78635722142, "time": 203, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306748939" }, { "job": 78635722190, "time": 279, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7306756015" }, { "job": 78635722171, "time": 297, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306757705" }, { "job": 78635722182, "time": 265, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7306754863" }, { "job": 78635722184, "time": 334, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306761396" }, { "job": 78635722156, "time": 226, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307940622" }, { "job": 78635722165, "time": 325, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7306762157" }, { "job": 78635722162, "time": 200, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307937041" }, { "job": 78635722183, "time": 389, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306768698" }, { "job": 78635443227, "time": 328, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306729063" }, { "job": 78635722155, "time": 136, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306742815" }, { "job": 78635722147, "time": 301, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306758270" }, { "job": 78635722145, "time": 288, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306756996" }, { "job": 78635722143, "time": 242, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306752677" } ], "_bioccheck": { "error": 2, "warning": 6, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/GRENITS", "_commit": { "id": "82b57b43aab244b2655712f30b0f8655c197061b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379735 }, "_maintainer": { "name": "Edward Morrissey", "email": "edward.morrissey@gmail.com", "login": "eled2", "description": "", "uuid": 1208890 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.12.0", "role": "Depends" }, { "package": "Rcpp", "version": ">= 0.8.6", "role": "Depends" }, { "package": "RcppArmadillo", "version": ">= 0.2.8", "role": "Depends" }, { "package": "ggplot2", "version": ">= 0.9.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "network", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.65.0", "bioc": "3.24" }, { "branch": "release", "version": "1.64.0", "bioc": "3.23" } ], "_topics": [ "networkinference", "generegulation", "timecourse", "graphandnetwork", "geneexpression", "network", "bayesian", "openblas", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 405, "source": "https://www.bioconductor.org/packages/stats/bioc/GRENITS" }, "_mentions": 8, "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GRENITS.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "analyse.output", "LinearNet", "mcmc.defaultParams_gauss", "mcmc.defaultParams_Linear", "mcmc.defaultParams_nonLinear", "mcmc.defaultParams_student", "NonLinearNet", "plotPriors", "read.chain", "ReplicatesNet_gauss", "ReplicatesNet_student" ], "_datasets": [ { "name": "Athaliana_ODE", "title": "Gene expression time series generated with ODE model", "object": "Athaliana_ODE", "file": "Athaliana_ODE.txt.gz", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3", "V4", "V5", "V6", "V7", "V8", "V9", "V10", "V11", "V12", "V13", "V14", "V15", "V16", "V17", "V18", "V19", "V20", "V21", "V22", "V23", "V24", "V25", "V26", "V27", "V28", "V29", "V30", "V31", "V32", "V33", "V34", "V35", "V36", "V37", "V38", "V39", "V40", "V41", "V42", "V43", "V44", "V45", "V46", "V47", "V48", "V49", "V50" ], "rows": 5, "table": true, "tojson": true }, { "name": "Athaliana_ODE_4NoiseReps", "title": "Gene expression time series generated with ODE model with added noise", "object": "Athaliana_ODE_4NoiseReps", "file": "Athaliana_ODE_4NoiseReps.txt.gz", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3", "V4", "V5", "V6", "V7", "V8", "V9", "V10", "V11", "V12", "V13", "V14", "V15", "V16", "V17", "V18", "V19", "V20", "V21", "V22", "V23", "V24", "V25", "V26", "V27", "V28", "V29", "V30", "V31", "V32", "V33", "V34", "V35", "V36", "V37", "V38", "V39", "V40", "V41", "V42", "V43", "V44", "V45", "V46", "V47", "V48", "V49", "V50", "V1.1", "V2.1", "V3.1", "V4.1", "V5.1", "V6.1", "V7.1", "V8.1", "V9.1", "V10.1", "V11.1", "V12.1", "V13.1", "V14.1", "V15.1", "V16.1", "V17.1", "V18.1", "V19.1", "V20.1", "V21.1", "V22.1", "V23.1", "V24.1", "V25.1", "V26.1", "V27.1", "V28.1", "V29.1", "V30.1", "V31.1", "V32.1", "V33.1", "V34.1", "V35.1", "V36.1", "V37.1", "V38.1", "V39.1", "V40.1", "V41.1", "V42.1", "V43.1", "V44.1", "V45.1", "V46.1", "V47.1", "V48.1", "V49.1", "V50.1", "V1.2", "V2.2", "V3.2", "V4.2", "V5.2", "V6.2", "V7.2", "V8.2", "V9.2", "V10.2", "V11.2", "V12.2", "V13.2", "V14.2", "V15.2", "V16.2", "V17.2", "V18.2", "V19.2", "V20.2", "V21.2", "V22.2", "V23.2", "V24.2", "V25.2", "V26.2", "V27.2", "V28.2", "V29.2", "V30.2", "V31.2", "V32.2", "V33.2", "V34.2", "V35.2", "V36.2", "V37.2", "V38.2", "V39.2", "V40.2", "V41.2", "V42.2", "V43.2", "V44.2", "V45.2", "V46.2", "V47.2", "V48.2", "V49.2", "V50.2", "V1.3", "V2.3", "V3.3", "V4.3", "V5.3", "V6.3", "V7.3", "V8.3", "V9.3", "V10.3", "V11.3", "V12.3", "V13.3", "V14.3", "V15.3", "V16.3", "V17.3", "V18.3", "V19.3", "V20.3", "V21.3", "V22.3", "V23.3", "V24.3", "V25.3", "V26.3", "V27.3", "V28.3", "V29.3", "V30.3", "V31.3", "V32.3", "V33.3", "V34.3", "V35.3", "V36.3", "V37.3", "V38.3", "V39.3", "V40.3", "V41.3", "V42.3", "V43.3", "V44.3", "V45.3", "V46.3", "V47.3", "V48.3", "V49.3", "V50.3" ], "rows": 5, "table": true, "tojson": true } ], "_help": [ { "page": "analyse.output", "title": "Analysis Plots", "topics": [ "analyse.output" ] }, { "page": "LockeData", "title": "Gene expression time series generated with ODE model", "topics": [ "Athaliana_ODE" ] }, { "page": "LockeDataError", "title": "Gene expression time series generated with ODE model with added noise", "topics": [ "Athaliana_ODE_4NoiseReps" ] }, { "page": "function_LinearNet", "title": "Dynamic Bayesian Network Inference Using Linear Interactions", "topics": [ "LinearNet" ] }, { "page": "defaultParams_gauss", "title": "Default Parameters for Linear Model with Gaussian distributed replicates", "topics": [ "mcmc.defaultParams_gauss" ] }, { "page": "defaultParams_linear", "title": "Default Parameters for Linear Model", "topics": [ "mcmc.defaultParams_Linear" ] }, { "page": "defaultParams_nonLinear", "title": "Default Parameters for non-Linear Model", "topics": [ "mcmc.defaultParams_nonLinear" ] }, { "page": "defaultParams_student", "title": "Default Parameters for Linear Model with Student distributed replicates", "topics": [ "mcmc.defaultParams_student" ] }, { "page": "function_NonLinearNet", "title": "Dynamic Bayesian Network Inference Using Non-Linear Interactions", "topics": [ "NonLinearNet" ] }, { "page": "plotPriors", "title": "Plot prior using parameter vector", "topics": [ "plotPriors" ] }, { "page": "readChains", "title": "Read MCMC Chains", "topics": [ "read.chain" ] }, { "page": "function_ReplicatesNet_gauss", "title": "Dynamic Bayesian Network Inference Using Linear Interactions and Gaussian Experimental Noise", "topics": [ "ReplicatesNet_gauss" ] }, { "page": "function_ReplicatesNet_student", "title": "Dynamic Bayesian Network Inference Using Linear Interactions and Student Experimental Noise", "topics": [ "ReplicatesNet_student" ] } ], "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "plyr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "rlang", "S7", "scales", "stringi", "stringr", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "GRENITS_package.Rnw", "filename": "GRENITS_package.pdf", "title": "GRENITS", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:19:37", "modified": "2013-11-01 20:19:37", "commits": 1 } ], "_score": 4.204119982655925, "_indexed": true, "_nocasepkg": "grenits", "_universes": [ "bioc", "eled2" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.65.0", "date": "2026-05-30T08:13:28.000Z", "distro": "noble", "arch": "aarch64", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "038e487c3e7818e1db3978f896e68297d9e2ce193f1e6dd017dcb1a0ec7e02cc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" }, { "r": "4.7.0", "os": "linux", "version": "1.65.0", "date": "2026-05-30T08:13:47.000Z", "distro": "noble", "arch": "x86_64", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "e779b7609e7d1537bf17e654b4c0d29c58bb25a93b6d28e457bc86811edd50c4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" }, { "r": "4.6.0", "os": "linux", "version": "1.65.0", "date": "2026-05-30T08:13:17.000Z", "distro": "noble", "arch": "aarch64", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "7054165811c16069e24c46deaa0748e5b16c157ef34425108f2590bd19d81f4b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" }, { "r": "4.6.0", "os": "linux", "version": "1.65.0", "date": "2026-05-30T08:14:18.000Z", "distro": "noble", "arch": "x86_64", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "30e130e4ecf16b512c1859f83d5f372adfd832c25c5737236e13d79d11977a81", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" }, { "r": "4.5.3", "os": "mac", "version": "1.65.0", "date": "2026-05-30T11:43:40.000Z", "arch": "aarch64", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "cb85a6a64128ef22a430fd86dd21ea46f8cf88802899d06f6a133cf59f02ddea", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" }, { "r": "4.5.3", "os": "mac", "version": "1.65.0", "date": "2026-05-30T08:13:57.000Z", "arch": "x86_64", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "11b5acb7485a77d0ef47b0b184f89684f7f5d9aea84408b211930168159ec8b1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" }, { "r": "4.6.0", "os": "mac", "version": "1.65.0", "date": "2026-05-30T11:43:12.000Z", "arch": "aarch64", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "39c612c394c6fc6af910b98259266babc068221fe15628a11d2c3cd63ba8d708", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" }, { "r": "4.6.0", "os": "mac", "version": "1.65.0", "date": "2026-05-30T08:14:38.000Z", "arch": "x86_64", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "0e433f3951da6fd37869d3ed37c957484a3a81d206012a77f6213255d8b537c7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" }, { "r": "4.6.0", "os": "wasm", "version": "1.65.0", "date": "2026-05-30T08:12:58.000Z", "arch": "emscripten", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "22e5bd53d87e999d04fac18bd975dc62e98b6317799779cf922a35ada00787f8", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" }, { "r": "4.7.0", "os": "win", "version": "1.65.0", "date": "2026-05-30T08:13:35.000Z", "arch": "x86_64", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "c41333851552091765f734779909f9ebf21ae42d46ff687c4e77cb865f1a68ed", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" }, { "r": "4.5.3", "os": "win", "version": "1.65.0", "date": "2026-05-30T08:12:20.000Z", "arch": "x86_64", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "71936ca4262b1a1cb2f84bf88ce1764e39b2c68952ba45e13463ce851b849c9b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" }, { "r": "4.6.0", "os": "win", "version": "1.65.0", "date": "2026-05-30T08:12:22.000Z", "arch": "x86_64", "commit": "82b57b43aab244b2655712f30b0f8655c197061b", "fileid": "ac0a0a761cae4be33d179f29f32d19212af6b4421ee5704b1f38d43db2c4b08a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678803040" } ] }