{ "_id": "6ad2069a1200a49930211f51", "Package": "CNORfeeder", "Type": "Package", "Title": "Integration of CellNOptR to add missing links", "Version": "1.52.0", "Author": "Federica Eduati [aut, cre]", "Maintainer": "Attila Gabor ", "Description": "This package integrates literature-constrained and\ndata-driven methods to infer signalling networks from\nperturbation experiments. It permits to extends a given network\nwith links derived from the data via various inference methods\nand uses information on physical interactions of proteins to\nguide and validate the integration of links.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "Date": "2022-05-11", "Authors@R": "c(\nperson(given = \"Federica\",\nfamily = \"Eduati\",\nrole = \"aut\"),\nperson(given = \"Enio\",\nfamily = \"Gjerga\",\nrole = \"ctb\"),\nperson(given = \"Attila\",\nfamily = \"Gabor\",\nrole = \"cre\",\nemail = \"attila.gabor@uni-heidelberg.de\")\n)", "biocViews": "CellBasedAssays, CellBiology, Proteomics, NetworkInference", "LazyLoad": "yes", "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 12:37:30 UTC", "RemoteUrl": "https://github.com/bioc/CNORfeeder", "RemoteRef": "RELEASE_3_23", "RemoteSha": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-16 11:07:18 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "CNORfeeder_1.52.0.tar.gz", "_fileid": "https://r2.ropensci.org/9a76a23be3164afccafa05b6af1caa359aa7cfff039f281f4b83482c78a90e99", "_filesize": 3608392, "_sha256": "9a76a23be3164afccafa05b6af1caa359aa7cfff039f281f4b83482c78a90e99", "_expires": "2027-01-24T11:12:23.000Z", "_created": "2026-10-16T11:07:18.000Z", "_published": "2026-10-16T11:12:25.941Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38891327479", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 6, "note": 17 }, "_upstream": "https://github.com/bioc/CNORfeeder", "_commit": { "id": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "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": 1777379850 }, "_maintainer": { "name": "Attila Gabor", "email": "attila.gabor@uni-heidelberg.de", "login": "gabora", "linkedin": "in/attila-g%C3%A1bor-94910524", "twitter": "@attila_gbr", "description": "Senior Comp-Bio scientist crafting R/Python code for comp. molecular biology/oncology, dedicated to advance healthcare with bioinformatics solutions", "uuid": 3891745 }, "_distro": "resolute", "_jobs": [ { "job": 116942580719, "time": 146, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "12042172936" }, { "job": 116942580693, "time": 261, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12042452280" }, { "job": 116942580841, "time": 185, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12041489488" }, { "job": 116942580799, "time": 110, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "12042600481" }, { "job": 116942580855, "time": 124, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12042192941" }, { "job": 116941371394, "time": 198, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12042142022" }, { "job": 116942580658, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12041932849" }, { "job": 116942580648, "time": 142, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12041967784" }, { "job": 116942580725, "time": 122, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "12042257840" }, { "job": 116942580635, "time": 124, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12041748683" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "graph", "role": "Depends" }, { "package": "CellNOptR", "version": ">= 1.4.0", "role": "Imports" }, { "package": "minet", "role": "Suggests" }, { "package": "Rgraphviz", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "MEIGOR", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.53.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.52.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "cellbasedassays", "cellbiology", "proteomics", "networkinference" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 477, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 580, "source": "https://www.bioconductor.org/packages/stats/bioc/CNORfeeder" }, "_mentions": 2, "_searchresults": 14, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CNORfeeder.html", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "Binference", "buildFeederObjectDynamic", "gaBinaryT1W", "identifyMisfitIndices", "integrateLinks", "linksRanking", "makeBTables", "mapBTables2model", "mapDDN2model", "MIinference", "runDynamicFeeder", "weighting" ], "_datasets": [ { "name": "cnolist", "title": "CNOlist", "object": "ToyModelPBCNOlist", "class": [ "CNOlist" ], "fields": [], "table": false, "tojson": false }, { "name": "CNOlistToy_Gene", "title": "", "object": "CNOlistToy_Gene", "class": [ "CNOlist" ], "fields": [], "table": false, "tojson": false }, { "name": "database", "title": "OmniPath PPI", "object": "database", "class": [ "matrix", "array" ], "fields": [], "rows": 12336, "table": true, "tojson": true }, { "name": "feederObject", "title": "Feeder Object", "object": "feederObject_toy", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "indices", "title": "Mis-fit indices", "object": "indices", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "integratedModel", "title": "Integrated Model", "object": "integratedModel_toy", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "model", "title": "Prior Knowledge Network", "object": "ToyModelPB", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "model", "title": "Prior Knowledge Network", "object": "ToyModel_Gene", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "PPINigraph", "title": "Protein-protein interaction netwrok", "object": "PPINigraph", "class": [ "igraph" ], "fields": [], "table": false, "tojson": false }, { "name": "simData", "title": "CNORode simuation data", "object": "simData_toy", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "UniprotIDdream", "title": "Uniprot identifiers for proteins in DreamModel", "object": "UniprotIDdream", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "CNORfeeder-package", "title": "R package to integrate literature-constrained and data-driven methods to infer signalling networks from perturbation experiments", "topics": [ "CNORfeeder-package", "CNORfeeder" ] }, { "page": "Binference", "title": "Bayesian network inference", "topics": [ "Binference" ] }, { "page": "buildFeederObjectDynamic", "title": "Building Feeder-Object for the integration to the PKN", "topics": [ "buildFeederObjectDynamic" ] }, { "page": "cnolist", "title": "CNOlist", "topics": [ "cnolist" ] }, { "page": "database", "title": "OmniPath PPI", "topics": [ "database" ] }, { "page": "feederObject", "title": "Feeder Object", "topics": [ "feederObject" ] }, { "page": "gaBinaryT1W", "title": "Genetic algorithm used to optimise a model differently weighting links", "topics": [ "gaBinaryT1W" ] }, { "page": "identifyMisfitIndices", "title": "Identifying indices of poorly fitted measurements", "topics": [ "identifyMisfitIndices" ] }, { "page": "indices", "title": "Mis-fit indices", "topics": [ "indices" ] }, { "page": "integratedModel", "title": "Integrated Model", "topics": [ "integratedModel" ] }, { "page": "integrateLinks", "title": "Integrating the new links to the PKN", "topics": [ "integrateLinks" ] }, { "page": "linksRanking", "title": "Ranking of links inferred from data", "topics": [ "linksRanking" ] }, { "page": "makeBTables", "title": "Make Boolean tables", "topics": [ "makeBTables" ] }, { "page": "mapBTables2model", "title": "Integrate Boolean tables with the model", "topics": [ "mapBTables2model" ] }, { "page": "mapDDN2model", "title": "Integrate data-drive network with the model", "topics": [ "mapDDN2model" ] }, { "page": "MIinference", "title": "Mutual information based network inference", "topics": [ "MIinference" ] }, { "page": "model", "title": "Prior Knowledge Network", "topics": [ "model" ] }, { "page": "PPINigraph", "title": "Protein-protein interaction netwrok", "topics": [ "PPINigraph" ] }, { "page": "runDynamicFeeder", "title": "Modelling the integrated PKN with CNORode", "topics": [ "runDynamicFeeder" ] }, { "page": "simData", "title": "CNORode simuation data", "topics": [ "simData" ] }, { "page": "UniprotIDdream", "title": "Uniprot identifiers for proteins in DreamModel", "topics": [ "UniprotIDdream" ] }, { "page": "weighting", "title": "Weight integrated links.", "topics": [ "weighting" ] } ], "_rundeps": [ "base64enc", "BH", "BiocGenerics", "bitops", "bslib", "cachem", "CellNOptR", "cli", "cpp11", "digest", "evaluate", "farver", "fastmap", "fontawesome", "fs", "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": "CNORfeeder-vignette.Rnw", "filename": "CNORfeeder-vignette.pdf", "title": "Main vignette:Playing with networks using CNORfeeder", "engine": "utils::Sweave", "headings": [ "Overview", "Installation", "Introduction", "Example", "Dynamic Feeder" ], "created": "2013-11-01 20:29:42", "modified": "2025-03-17 15:21:05", "commits": 6 } ], "_score": 3.7481880270062007, "_indexed": false, "_nocasepkg": "cnorfeeder", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/CNORfeeder", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.52.0", "date": "2026-10-16T11:11:11.000Z", "distro": "resolute", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "https://r2.ropensci.org/3c7dbe2a0133a3adc79389c7c2dff31c63d6321c821d1a22ac3905d588103e1f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38891327479" }, { "r": "4.6.1", "os": "linux", "version": "1.52.0", "date": "2026-10-16T11:10:20.000Z", "distro": "resolute", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "https://r2.ropensci.org/58e90413e6e7fa7f69f628787af54a385e51c49e421184ed8e5500ff275aa424", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38891327479" }, { "r": "4.5.3", "os": "mac", "version": "1.52.0", "date": "2026-10-16T11:10:44.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "https://r2.ropensci.org/2ba30c3e8fc60910f825358acbbf63d1b1d8b147ee0e66499e3209e1be8ab0e4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38891327479" }, { "r": "4.6.1", "os": "mac", "version": "1.52.0", "date": "2026-10-16T11:09:56.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "https://r2.ropensci.org/a12eec0755964519d38b4455fea6b42777648208eaa17ce670d166c201da45cb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38891327479" }, { "r": "4.6.0", "os": "wasm", "version": "1.52.0", "date": "2026-10-16T11:09:54.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "https://r2.ropensci.org/46ca2937929214ef30ebaef07dc9a72c516c56958298e36b7f5dd6bd73082fb5", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38891327479" }, { "r": "4.7.0", "os": "win", "version": "1.52.0", "date": "2026-10-16T11:09:01.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "https://r2.ropensci.org/860bfd23cdaaebe29a0c6270abea0baad4961d047fc57677d9d1ccd0072c9743", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38891327479" }, { "r": "4.5.3", "os": "win", "version": "1.52.0", "date": "2026-10-16T11:08:51.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "https://r2.ropensci.org/41e27ce0f810cec564baa712266b602cf511ad2a1c52eef19a6675cc24150640", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38891327479" }, { "r": "4.6.1", "os": "win", "version": "1.52.0", "date": "2026-10-16T11:08:56.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "https://r2.ropensci.org/ed5a1946c4910708f3376566fad6b89a21d3ba69b952733741a05a2d268e89e9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38891327479" } ] }