{ "_id": "6ab7a8bb99f7aa8c6aa33785", "Package": "ternarynet", "Version": "1.56.0", "Date": "2024-02-19", "Title": "Ternary Network Estimation", "Description": "Gene-regulatory network (GRN) modeling seeks to infer\ndependencies between genes and thereby provide insight into the\nregulatory relationships that exist within a cell. This package\nprovides a computational Bayesian approach to GRN estimation\nfrom perturbation experiments using a ternary network model, in\nwhich gene expression is discretized into one of 3 states: up,\nunchanged, or down). The ternarynet package includes a parallel\nimplementation of the replica exchange Monte Carlo algorithm\nfor fitting network models, using MPI.", "Author": "Matthew N. McCall , Anthony Almudevar\n, David Burton\n, Harry Stern\n", "Authors@R": "c(\nperson(\"McCall\",\"Matthew\",\nemail=\"mccallm@gmail.com\",\nrole=c(\"aut\",\"cre\")),\nperson(\"Almudevar\",\"Anthony\",\nemail=\"Anthony_Almudevar@urmc.rochester.edu\",\nrole=c(\"aut\")),\nperson(\"Burton\",\"David\",\nemail=\"David_Burton@urmc.rochester.edu\",\nrole=c(\"aut\")),\nperson(\"Stern\",\"Harry\",\nemail=\"harry.stern@rochester.edu\",\nrole=c(\"aut\")))", "License": "GPL (>= 2)", "biocViews": "Software, CellBiology, GraphAndNetwork, Network, Bayesian", "git_url": "https://git.bioconductor.org/packages/ternarynet", "git_branch": "master", "git_last_commit": "6fb06d2", "git_last_commit_date": "2020-10-27", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-09-26 11:07:50 UTC", "User": "root" }, "Maintainer": "McCall N. Matthew ", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:36:17 UTC", "RemoteUrl": "https://github.com/bioc/ternarynet", "RemoteRef": "RELEASE_3_23", "RemoteSha": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "_user": "bioc-release", "_type": "src", "_file": "ternarynet_1.56.0.tar.gz", "_fileid": "https://r2.ropensci.org/2462133a4add7d4223fa7c0752443b43c5066cabf6ffe631714332719be0d455", "_filesize": 290481, "_sha256": "2462133a4add7d4223fa7c0752443b43c5066cabf6ffe631714332719be0d455", "_expires": "2027-01-04T11:12:57.000Z", "_created": "2026-09-26T11:07:50.000Z", "_published": "2026-09-26T11:12:59.408Z", "_bioccheck": { "error": 0, "warning": 1, "note": 11 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835", "_status": "success", "_upstream": "https://github.com/bioc/ternarynet", "_commit": { "id": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379777 }, "_maintainer": { "name": "McCall N. Matthew", "email": "mccallm@gmail.com", "login": "mccallm", "description": "", "uuid": 3731477 }, "_distro": "resolute", "_jobs": [ { "job": 108392888953, "time": 154, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "10905470028" }, { "job": 108392888906, "time": 149, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "10904504061" }, { "job": 108392888958, "time": 269, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10904449317" }, { "job": 108392888905, "time": 139, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10905470012" }, { "job": 108392889027, "time": 200, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10904666568" }, { "job": 108392888964, "time": 92, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10904474122" }, { "job": 108392888922, "time": 204, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10904489226" }, { "job": 108392889021, "time": 116, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10905230725" }, { "job": 108392888913, "time": 252, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10904812516" }, { "job": 108392333011, "time": 236, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10904229808" }, { "job": 108392888930, "time": 131, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10905270546" }, { "job": 108392888996, "time": 250, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "10905135867" }, { "job": 108392888956, "time": 153, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10905046928" }, { "job": 108392889080, "time": 145, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10904772170" }, { "job": 108392889008, "time": 232, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10905036165" }, { "job": 108392888972, "time": 123, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10905115822" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "Rmpi", "role": "Enhances" }, { "package": "snow", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.57.0", "bioc": "3.24" }, { "branch": "release", "version": "1.56.0", "bioc": "3.23" } ], "_topics": [ "software", "cellbiology", "graphandnetwork", "network", "bayesian", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 468, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 472, "source": "https://www.bioconductor.org/packages/stats/bioc/ternarynet" }, "_searchresults": 5, "_rbuild": "4.6.1", "_assets": [ "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/ternarynet.html" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "attractorSummary", "backupStage", "backupStage<-", "beta0", "beta0<-", "chi0", "chi0<-", "degreeObjMin", "degreeObjMin<-", "degreeObjs", "degreeObjs<-", "delta", "delta<-", "edgePenalty", "edgePenalty<-", "epsilon", "epsilon<-", "experimentNames", "experimentNames<-", "finalTemperature", "finalTemperature<-", "geneNames", "geneNames<-", "graphObjMin", "graphObjMin<-", "graphObjs", "graphObjs<-", "graphPosterior", "inputParams", "inputParams<-", "m0", "m0<-", "maxDegree", "maxDegree<-", "maxStage", "maxStage<-", "maxTransition", "maxTransition<-", "minScore", "minScore<-", "ne", "ne<-", "neighborDegree", "neighborDegree<-", "newScore", "newScore<-", "pAddParent", "pAddParent<-", "parallelFit", "perturbationObj", "perturbationObj<-", "perturbationType", "perturbationType<-", "pExchangeParent", "pExchangeParent<-", "plotFit", "plotPost", "plotTraces", "pNeighborhood", "pNeighborhood<-", "predictAttractor", "rho", "rho<-", "scores", "scores<-", "scoreType", "scoreType<-", "simulateSteadyState", "stageCount", "stageCount<-", "steadyStateObj", "steadyStateObj<-", "tableObjMin", "tableObjMin<-", "tableObjs", "tableObjs<-", "ternaryFit", "ternaryFitParameters", "ternaryPost", "tnetfit", "tnetpost", "traces", "traces<-", "xSeed", "xSeed<-" ], "_help": [ { "page": "attractorSummary", "title": "Summarize Attractors", "topics": [ "attractorSummary" ] }, { "page": "graphPosterior", "title": "Network Topology", "topics": [ "graphPosterior" ] }, { "page": "parallelFit", "title": "Fit ternary network models using parallel tempering", "topics": [ "parallelFit" ] }, { "page": "plotFit", "title": "Network Fit Plot", "topics": [ "plotFit" ] }, { "page": "plotPost", "title": "Network Posterior Plot", "topics": [ "plotPost" ] }, { "page": "plotTraces", "title": "Network Fit Traces", "topics": [ "plotTraces" ] }, { "page": "predictAttractor", "title": "Predict the attractor(s) resulting from a given perturbation", "topics": [ "predictAttractor" ] }, { "page": "simulateSteadyState", "title": "Simulate Steady State Data", "topics": [ "simulateSteadyState" ] }, { "page": "ternaryFit-class", "title": "Ternary Network Fit", "topics": [ "class:ternaryFit", "degreeObjMin", "degreeObjMin,ternaryFit-method", "degreeObjMin<-", "degreeObjMin<-,ternaryFit-method", "dim,ternaryFit-method", "experimentNames", "experimentNames,ternaryFit-method", "experimentNames<-", "experimentNames<-,ternaryFit-method", "finalTemperature", "finalTemperature,ternaryFit-method", "finalTemperature<-", "finalTemperature<-,ternaryFit-method", "geneNames", "geneNames,ternaryFit-method", "geneNames<-", "geneNames<-,ternaryFit-method", "graphObjMin", "graphObjMin,ternaryFit-method", "graphObjMin<-", "graphObjMin<-,ternaryFit-method", "initialize,ternaryFit-method", "inputParams", "inputParams,ternaryFit-method", "inputParams<-", "inputParams<-,ternaryFit-method", "minScore", "minScore,ternaryFit-method", "minScore<-", "minScore<-,ternaryFit-method", "newScore", "newScore,ternaryFit-method", "newScore<-", "newScore<-,ternaryFit-method", "perturbationObj", "perturbationObj,ternaryFit-method", "perturbationObj<-", "perturbationObj<-,ternaryFit-method", "show,ternaryFit-method", "stageCount", "stageCount,ternaryFit-method", "stageCount<-", "stageCount<-,ternaryFit-method", "steadyStateObj", "steadyStateObj,ternaryFit-method", "steadyStateObj<-", "steadyStateObj<-,ternaryFit-method", "tableObjMin", "tableObjMin,ternaryFit-method", "tableObjMin<-", "tableObjMin<-,ternaryFit-method", "ternaryFit", "ternaryFit-class", "ternaryFit-methods", "traces", "traces,ternaryFit-method", "traces<-", "traces<-,ternaryFit-method", "xSeed", "xSeed,ternaryFit-method", "xSeed<-", "xSeed<-,ternaryFit-method" ] }, { "page": "ternaryFitParameters-class", "title": "Ternary Network Fitting Parameters", "topics": [ "backupStage", "backupStage,ternaryFitParameters-method", "backupStage<-", "backupStage<-,ternaryFitParameters-method", "beta0", "beta0,ternaryFitParameters-method", "beta0<-", "beta0<-,ternaryFitParameters-method", "chi0", "chi0,ternaryFitParameters-method", "chi0<-", "chi0<-,ternaryFitParameters-method", "class:ternaryFitParameters", "delta", "delta,ternaryFitParameters-method", "delta<-", "delta<-,ternaryFitParameters-method", "edgePenalty", "edgePenalty,ternaryFitParameters-method", "edgePenalty<-", "edgePenalty<-,ternaryFitParameters-method", "epsilon", "epsilon,ternaryFitParameters-method", "epsilon<-", "epsilon<-,ternaryFitParameters-method", "initialize,ternaryFitParameters-method", "m0", "m0,ternaryFitParameters-method", "m0<-", "m0<-,ternaryFitParameters-method", "maxDegree", "maxDegree,ternaryFitParameters-method", "maxDegree<-", "maxDegree<-,ternaryFitParameters-method", "maxStage", "maxStage,ternaryFitParameters-method", "maxStage<-", "maxStage<-,ternaryFitParameters-method", "maxTransition", "maxTransition,ternaryFitParameters-method", "maxTransition<-", "maxTransition<-,ternaryFitParameters-method", "ne", "ne,ternaryFitParameters-method", "ne<-", "ne<-,ternaryFitParameters-method", "neighborDegree", "neighborDegree,ternaryFitParameters-method", "neighborDegree<-", "neighborDegree<-,ternaryFitParameters-method", "pAddParent", "pAddParent,ternaryFitParameters-method", "pAddParent<-", "pAddParent<-,ternaryFitParameters-method", "perturbationType", "perturbationType,ternaryFitParameters-method", "perturbationType<-", "perturbationType<-,ternaryFitParameters-method", "pExchangeParent", "pExchangeParent,ternaryFitParameters-method", "pExchangeParent<-", "pExchangeParent<-,ternaryFitParameters-method", "pNeighborhood", "pNeighborhood,ternaryFitParameters-method", "pNeighborhood<-", "pNeighborhood<-,ternaryFitParameters-method", "rho", "rho,ternaryFitParameters-method", "rho<-", "rho<-,ternaryFitParameters-method", "scoreType", "scoreType,ternaryFitParameters-method", "scoreType<-", "scoreType<-,ternaryFitParameters-method", "show,ternaryFitParameters-method", "ternaryFitParameters", "ternaryFitParameters-class", "ternaryFitParameters-methods" ] }, { "page": "ternaryPost-class", "title": "Ternary Network Posterior", "topics": [ "class:ternaryPost", "degreeObjs", "degreeObjs,ternaryPost-method", "degreeObjs<-", "degreeObjs<-,ternaryPost-method", "dim,ternaryPost-method", "experimentNames,ternaryPost-method", "experimentNames<-,ternaryPost-method", "geneNames,ternaryPost-method", "geneNames<-,ternaryPost-method", "graphObjs", "graphObjs,ternaryPost-method", "graphObjs<-", "graphObjs<-,ternaryPost-method", "initialize,ternaryPost-method", "inputParams,ternaryPost-method", "inputParams<-,ternaryPost-method", "perturbationObj,ternaryPost-method", "perturbationObj<-,ternaryPost-method", "scores", "scores,ternaryPost-method", "scores<-", "scores<-,ternaryPost-method", "show,ternaryPost-method", "steadyStateObj,ternaryPost-method", "steadyStateObj<-,ternaryPost-method", "tableObjs", "tableObjs,ternaryPost-method", "tableObjs<-", "tableObjs<-,ternaryPost-method", "ternaryPost", "ternaryPost-class", "ternaryPost-methods" ] }, { "page": "tnetfit", "title": "Ternary Network Fitting", "topics": [ "tnetfit" ] }, { "page": "tnetpost", "title": "Ternary Network Posterior Sampling", "topics": [ "tnetpost" ] } ], "_rundeps": [ "BH", "BiocParallel", "cli", "codetools", "cpp11", "formatR", "futile.logger", "futile.options", "glue", "igraph", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "rlang", "snow", "vctrs" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "ternarynet.Rnw", "filename": "ternarynet.pdf", "title": "ternarynet: A Computational Bayesian Approach to Ternary Network Estimation", "engine": "utils::Sweave", "headings": [ "Introduction", "Getting Started", "Session Info" ], "created": "2013-11-01 20:23:40", "modified": "2021-04-15 18:13:14", "commits": 4 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "ternarynet", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/ternarynet", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.56.0", "date": "2026-09-26T11:10:16.000Z", "distro": "resolute", "arch": "aarch64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/be8704c21244859a649c68b7f3873438a0ca48dc32a6784868ab161c02866263", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.7.0", "os": "linux", "version": "1.56.0", "date": "2026-09-26T11:12:12.000Z", "distro": "resolute", "arch": "x86_64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/62de86f73ca521fea0abdb6cd3cda9a19df6856240d60a7876a5bde0f737a5dc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.6.1", "os": "linux", "version": "1.56.0", "date": "2026-09-26T11:10:10.000Z", "distro": "resolute", "arch": "aarch64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/9b0520478a7930f526eb287d4858ccbcfe8e0a20007af553cfd3ebb65c64bade", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.6.1", "os": "linux", "version": "1.56.0", "date": "2026-09-26T11:11:02.000Z", "distro": "resolute", "arch": "x86_64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/abdb0098af1466840af4052996dae1d3beaadf8411227170afa9f2e6aeb08962", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.5.3", "os": "mac", "version": "1.56.0", "date": "2026-09-26T11:09:15.000Z", "arch": "aarch64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/be47620ca898c66507565fbed0871dd406e977bb4b30fb253247bcceee39eeba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.5.3", "os": "mac", "version": "1.56.0", "date": "2026-09-26T11:10:34.000Z", "arch": "x86_64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/3ef5d981c2b659eaed7e3cf67bc300870520c85f57f23a9002d8f6eef1d35a63", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.6.1", "os": "mac", "version": "1.56.0", "date": "2026-09-26T11:09:35.000Z", "arch": "aarch64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/6ceeb27b110fd10815b8d5e599fdd9fb4cd46be4f4e04d132f8633c6d030d6bb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.6.1", "os": "mac", "version": "1.56.0", "date": "2026-09-26T11:11:09.000Z", "arch": "x86_64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/d7a2389dd5704ac84f0f498fcc872876d8e9b2b3787947e9b8d4f7f7b909a7c9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.6.0", "os": "wasm", "version": "1.56.0", "date": "2026-09-26T11:10:17.000Z", "arch": "emscripten", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/fc68586e5b943a01a897ac49cd59f76013bcbfe967615903872a369dae26761d", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.7.0", "os": "win", "version": "1.56.0", "date": "2026-09-26T11:11:32.000Z", "arch": "aarch64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/851c5836295948e17a3b24b092f175c49d250fe52ceff9218b258ad57e6d9e37", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.7.0", "os": "win", "version": "1.56.0", "date": "2026-09-26T11:09:17.000Z", "arch": "x86_64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/1eb8a2effd1df3f055c40c9fcfcd45b7762d8d631c6dc09bf12e403f7b711e77", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.5.3", "os": "win", "version": "1.56.0", "date": "2026-09-26T11:09:49.000Z", "arch": "x86_64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/71bd5c7e579dd2cdefdb61f2603964192f178cc26b184fd1168836dbefd31628", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.6.1", "os": "win", "version": "1.56.0", "date": "2026-09-26T11:11:14.000Z", "arch": "aarch64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/4dd0829b9f369c3e9031c623328367727f5f189232295cff1609e4ca43d88bd5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" }, { "r": "4.6.1", "os": "win", "version": "1.56.0", "date": "2026-09-26T11:09:17.000Z", "arch": "x86_64", "commit": "8a6bb8df77f1c7fb219cfb5e523096b5df31ab99", "fileid": "https://r2.ropensci.org/5e6735bac9628c902a3e11e40e96bec9dc80905e0474950c2e14190015dbbb52", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36237634835" } ] }