{ "_id": "6ae320598d250e7ad09efeb3", "Package": "CNORode", "Type": "Package", "Title": "ODE add-on to CellNOptR", "Version": "1.54.0", "Date": "2022-03-22", "Authors@R": "c(\nperson(given = \"David\",\nfamily = \"Henriques\",\nrole = \"aut\"),\nperson(given = \"Thomas\",\nfamily = \"Cokelaer\",\nrole = c(\"aut\")),\nperson(given = \"Federica\",\nfamily = \"Eduati\",\nrole = \"ctb\"),\nperson(given = \"Enio\",\nfamily = \"Gjerga\",\nrole = \"ctb\"),\nperson(given = \"Attila\",\nfamily = \"Gabor\",\nrole = \"ctb\"),\nperson(given = \"Aurelien\",\nfamily = \"Dugourd\",\nrole = \"cre\",\nemail = \"dugourd@ebi.ac.uk\")\n)", "Author": "David Henriques, Thomas Cokelaer, Attila Gabor, Federica\nEduati, Enio Gjerga", "Description": "Logic based ordinary differential equation (ODE) add-on to\nCellNOptR.", "License": "GPL-2", "LazyLoad": "yes", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, CellBasedAssays, CellBiology, Proteomics,\nBioinformatics, TimeCourse", "RoxygenNote": "7.1.2", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:36:58 UTC", "RemoteUrl": "https://github.com/bioc/CNORode", "RemoteRef": "RELEASE_3_23", "RemoteSha": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-29 10:18:42 UTC", "User": "root" }, "Maintainer": "Aurelien Dugourd ", "_user": "bioc-release", "_type": "src", "_file": "CNORode_1.54.0.tar.gz", "_fileid": "https://r2.ropensci.org/151f2d7667de7656a0e90cf5246920f3105851267d9a44e3d0e63df170a08fae", "_filesize": 1240726, "_sha256": "151f2d7667de7656a0e90cf5246920f3105851267d9a44e3d0e63df170a08fae", "_expires": "2027-02-06T10:30:47.000Z", "_created": "2026-10-29T10:18:42.000Z", "_published": "2026-10-29T10:30:49.434Z", "_upstream": "https://github.com/bioc/CNORode", "_status": "success", "_maintainer": { "name": "Aurelien Dugourd", "email": "dugourd@ebi.ac.uk", "login": "adugourd", "twitter": "@DugourdAjf", "description": "Senior staff Scientist @saezlab @embl-ebi. I lead the development and application of methods to extract interpretable mechanistic insights from multi-omic data.", "uuid": 16302934 }, "_jobs": [ { "job": 123389041853, "time": 161, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "12889053916" }, { "job": 123389041941, "time": 162, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "12889397983" }, { "job": 123389041839, "time": 230, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12889681883" }, { "job": 123389041793, "time": 156, "config": "linux-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12890255781" }, { "job": 123389041816, "time": 210, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12888924748" }, { "job": 123389042092, "time": 131, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "12889073719" }, { "job": 123389041855, "time": 436, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "12889094242" }, { "job": 123389041835, "time": 145, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12889976200" }, { "job": 123389042000, "time": 368, "config": "macos-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12890136214" }, { "job": 123386449558, "time": 343, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12889776029" }, { "job": 123389041712, "time": 119, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12888844853" }, { "job": 123389042135, "time": 270, "config": "windows-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "12889901727" }, { "job": 123389041879, "time": 169, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12890280488" }, { "job": 123389041871, "time": 174, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "12889601825" }, { "job": 123389041916, "time": 260, "config": "windows-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12888639737" }, { "job": 123389041982, "time": 162, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12889417407" } ], "_bioccheck": { "error": 1, "warning": 7, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465", "_commit": { "id": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "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": 1777379818 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "CellNOptR", "role": "Depends" }, { "package": "genalg", "role": "Depends" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "doParallel", "role": "Enhances" }, { "package": "foreach", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-50", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.55.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.54.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "immunooncology", "cellbasedassays", "cellbiology", "proteomics", "bioinformatics", "timecourse" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 481, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 550, "source": "https://www.bioconductor.org/packages/stats/bioc/CNORode" }, "_mentions": 5, "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CNORode.html", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "createLBodeContPars", "defaultParametersGA", "defaultParametersSSm", "getLBodeContObjFunction", "getLBodeDataSim", "getLBodeMINLPObjFunction", "getLBodeModelSim", "getLBodeSimFunction", "getStates", "incidence2Adjacency", "minlpLBodeSSm", "parEstimationLBode", "parEstimationLBodeGA", "parEstimationLBodeSSm", "plotLBodeFitness", "plotLBodeModelSim", "runCNORode", "simdata2cnolist", "simulate" ], "_datasets": [ { "name": "cnodata", "title": "A cnodata from CellNoptR", "object": "CNOlist_ToyPB", "file": "CNOlist_ToyPB.RData", "class": [ "CNOlist" ], "fields": [], "table": false, "tojson": false }, { "name": "cnolist", "title": "A cnolist from CellNoptR", "object": "MD-ToyPB", "file": "MD-ToyPB.RData", "class": [ "CNOlist" ], "fields": [], "table": false, "tojson": false }, { "name": "cnolistCNORodeExample", "title": "A cnolist from CellNoptR", "object": "ToyCNOlist", "file": "ToyCNOlist.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "indices", "title": "Indices that relate cnolist to model", "object": "ToyIndices", "file": "ToyIndices.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "model", "title": "A model from CellNoptR", "object": "ToyModel", "file": "ToyModel.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "pknmodel", "title": "A pknmodel from CellNoptR", "object": "PKN_ToyPB", "file": "PKN_ToyPB.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "pknmodel", "title": "A pknmodel from CellNoptR", "object": "PKN-ToyPB", "file": "PKN-ToyPB.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "cnodata", "title": "A cnodata from CellNoptR", "topics": [ "cnodata" ] }, { "page": "cnolist", "title": "A cnolist from CellNoptR", "topics": [ "cnolist" ] }, { "page": "cnolistCNORodeExample", "title": "A cnolist from CellNoptR", "topics": [ "cnolistCNORodeExample" ] }, { "page": "CNORode-package", "title": "Logic based ODE extension for CellNOptR", "topics": [ "CNORode" ] }, { "page": "createLBodeContPars", "title": "Create a list with ODE parameter information needed to perform parameter estimation", "topics": [ "createLBodeContPars" ] }, { "page": "crossvalidateODE", "title": "Crossvalidate ODE model", "topics": [ "crossvalidateODE" ] }, { "page": "defaultParametersGA", "title": "Create default options to perform parameter estimation with a genetic algorithm.", "topics": [ "defaultParametersGA" ] }, { "page": "defaultParametersSSm", "title": "Create default options to perform parameter estimation with scatter search meta-heuristic.", "topics": [ "defaultParametersSSm" ] }, { "page": "getLBodeContObjFunction", "title": "Returns the objective function to perform parameter estimation.", "topics": [ "getLBodeContObjFunction" ] }, { "page": "getLBodeDataSim", "title": "Simulate value signals a CNO list With Logic-Based ODEs.", "topics": [ "getLBodeDataSim" ] }, { "page": "getLBodeMINLPObjFunction", "title": "Get the objective function to evaluate the fitness of a given model structure and set of parameters.", "topics": [ "getLBodeMINLPObjFunction" ] }, { "page": "getLBodeModelSim", "title": "Simulate the logic-based ODE model", "topics": [ "getLBodeModelSim" ] }, { "page": "getLBodeSimFunction", "title": "Get a function to simulate a logic based ODE model.", "topics": [ "getLBodeSimFunction" ] }, { "page": "getStates", "title": "Find which species in the model are states.", "topics": [ "getStates" ] }, { "page": "incidence2Adjacency", "title": "Convert an incidence matrix into an adjacency matrix.", "topics": [ "incidence2Adjacency" ] }, { "page": "indices", "title": "Indices that relate cnolist to model", "topics": [ "indices" ] }, { "page": "minlpLBodeSSm", "title": "Search for the best combination of continuous parameters and logic gates.", "topics": [ "minlpLBodeSSm" ] }, { "page": "model", "title": "A model from CellNoptR", "topics": [ "model" ] }, { "page": "parEstimationLBode", "title": "Perform parameter estimation using a genetic algorithm (package genalg) or ssm (if package essm available).", "topics": [ "parEstimationLBode" ] }, { "page": "parEstimationLBodeGA", "title": "Perform parameter estimation using a genetic algorithm (package genalg).", "topics": [ "parEstimationLBodeGA" ] }, { "page": "parEstimationLBodeSSm", "title": "Perform parameter estimation using essR.", "topics": [ "parEstimationLBodeSSm" ] }, { "page": "pknmodel", "title": "A pknmodel from CellNoptR", "topics": [ "pknmodel" ] }, { "page": "plotLBodeFitness", "title": "Plot data against simulated values.", "topics": [ "plotLBodeFitness" ] }, { "page": "plotLBodeModelSim", "title": "Simulate the model and plot the obtained with the different experimental conditions.", "topics": [ "plotLBodeModelSim" ] }, { "page": "runCNORode", "title": "runCNORode", "topics": [ "runCNORode" ] }, { "page": "simdata2cnolist", "title": "converts output of getLBodeModelSim to cnolist", "topics": [ "simdata2cnolist" ] }, { "page": "simulate", "title": "Simulate value signals a CNO list With Logic-Based ODEs.", "topics": [ "simulate" ] } ], "_readme": "https://github.com/bioc/CNORode/raw/RELEASE_3_23/README.md", "_rundeps": [ "base64enc", "BH", "BiocGenerics", "bitops", "bslib", "cachem", "CellNOptR", "cli", "cpp11", "digest", "evaluate", "farver", "fastmap", "fontawesome", "fs", "genalg", "generics", "ggplot2", "glue", "graph", "gtable", "highr", "htmltools", "igraph", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "memoise", "mime", "pkgconfig", "R6", "rappdirs", "RBGL", "RColorBrewer", "RCurl", "Rgraphviz", "rlang", "rmarkdown", "S7", "sass", "scales", "stringi", "stringr", "tinytex", "vctrs", "viridisLite", "withr", "xfun", "XML", "yaml" ], "_vignettes": [ { "source": "CNORode-vignette.Rmd", "filename": "CNORode-vignette.html", "title": "Training Signalling Pathway Maps to Biochemical Data with Logic-Based Ordinary Differential Equations", "author": "David Henriques, Thomas Cokelaer, Enio Gjerga, Attila Gabor", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Quick Start", "Crossvalidation" ], "created": "2024-01-24 09:48:27", "modified": "2024-02-27 09:25:40", "commits": 3 } ], "_score": 5.176091259055681, "_indexed": false, "_nocasepkg": "cnorode", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/CNORode", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.54.0", "date": "2026-10-29T10:21:10.000Z", "distro": "resolute", "arch": "aarch64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/99644338547e8f1674c24e3cf053adc660a68419d84f2d184c5414655d48c487", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.7.0", "os": "linux", "version": "1.54.0", "date": "2026-10-29T10:22:19.000Z", "distro": "resolute", "arch": "x86_64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/2982db474aaa458e1265eedb353242c06dc5599bb0f9b3365a644bd4c41a6cd8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.6.1", "os": "linux", "version": "1.54.0", "date": "2026-10-29T10:21:05.000Z", "distro": "resolute", "arch": "aarch64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/490a1a3a3564f62468083876b024a359fffedf1469d001db4e3587ab72a8826a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.6.1", "os": "linux", "version": "1.54.0", "date": "2026-10-29T10:21:44.000Z", "distro": "resolute", "arch": "x86_64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/a70a4d12079c6118981bd9792dcb5238aeb09d8649cbb72ebabb9a40554bdc6d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.5.3", "os": "mac", "version": "1.54.0", "date": "2026-10-29T10:20:39.000Z", "arch": "aarch64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/659f1f6dd7e52c17943a3f3c47adf6316a847cef7fd7ce72fd454e06fae8dec2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.5.3", "os": "mac", "version": "1.54.0", "date": "2026-10-29T10:23:25.000Z", "arch": "x86_64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/fae676eb756cb96daeed7189741c27c709d161c29222e51ac37c248a32e1cbd0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.6.1", "os": "mac", "version": "1.54.0", "date": "2026-10-29T10:20:45.000Z", "arch": "aarch64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/d3d3eb0b4f4678103338035ec0891f0d5fd192e4dd8b0ba2aa344f6c3900615a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.6.1", "os": "mac", "version": "1.54.0", "date": "2026-10-29T10:22:44.000Z", "arch": "x86_64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/6416a82d952325de23a67f6749fdfac4a2568ed155c114728b43fdfa0e3c2c3a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.6.0", "os": "wasm", "version": "1.54.0", "date": "2026-10-29T10:20:58.000Z", "arch": "emscripten", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/8d0f9c05940fcd9986ad4645b550f30b2e21472bceeab0a0431c8cd49feb33ce", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.7.0", "os": "win", "version": "1.54.0", "date": "2026-10-29T10:22:17.000Z", "arch": "aarch64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/913bb85adc06a5159f699aab02fc6591f61b353a372cf99c5e78384db4e8c96c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.7.0", "os": "win", "version": "1.54.0", "date": "2026-10-29T10:20:11.000Z", "arch": "x86_64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/f994274fa541fa8fe335538abbba95c0cd1ebc3a443241e005788b176798666d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.5.3", "os": "win", "version": "1.54.0", "date": "2026-10-29T10:20:40.000Z", "arch": "x86_64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/4d721b56939cccb776e7628adee3d4996a9488a5ffd6b7a4c4fbc868b19bfc39", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.6.1", "os": "win", "version": "1.54.0", "date": "2026-10-29T10:22:10.000Z", "arch": "aarch64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/916f5597d4d20daf977cecaa983ca790dbef2c30468223ecefef39bd22e6ec07", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" }, { "r": "4.6.1", "os": "win", "version": "1.54.0", "date": "2026-10-29T10:20:22.000Z", "arch": "x86_64", "commit": "bd9daab77f934f8859dafcb7c79dcec78ca41634", "fileid": "https://r2.ropensci.org/9d9fff014acec818f56888614ee79244db684f8f277983206bdc207b8aa59ddb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/40855785465" } ] }