{ "_id": "6a339fd03efcd9bda43a81c8", "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": "https://bioc-release.r-universe.dev", "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": "2026-06-18 07:16:13 UTC", "User": "root" }, "MD5sum": "514939d630907722e0eba7143d5d33af", "_user": "bioc-release", "_type": "src", "_file": "CNORfeeder_1.52.0.tar.gz", "_fileid": "3eb67d472f2c78fd79847949bdb660cbb706e77b0ba0c58054281e92a3618622", "_filesize": 3604713, "_sha256": "3eb67d472f2c78fd79847949bdb660cbb706e77b0ba0c58054281e92a3618622", "_created": "2026-06-18T07:16:13.000Z", "_published": "2026-06-18T07:35:44.149Z", "_jobs": [ { "job": 82075284322, "time": 183, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7716645705" }, { "job": 82075284300, "time": 247, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7716665410" }, { "job": 82075284340, "time": 250, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7716666899" }, { "job": 82075284292, "time": 164, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7716941437" }, { "job": 82075284299, "time": 128, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7716930573" }, { "job": 82074724172, "time": 220, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7716589039" }, { "job": 82075284271, "time": 136, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7716631841" }, { "job": 82075284293, "time": 149, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7716636011" }, { "job": 82075284310, "time": 120, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7716627179" }, { "job": 82075284323, "time": 144, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7716634350" } ], "_bioccheck": { "error": 0, "warning": 6, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27743058544", "_status": "success", "_host": "GitHub-Actions", "_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": "noble", "_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" }, { "branch": "release", "version": "1.52.0", "bioc": "3.23" } ], "_topics": [ "cellbasedassays", "cellbiology", "proteomics", "networkinference" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 2, "_searchresults": 14, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CNORfeeder.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_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": "2026-06-18T07:19:51.000Z", "distro": "noble", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "332e7ad1dcc87cfc707fcf44748422a1de787e18191beb6bfc43c9ba3b9ce492", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27743058544" }, { "r": "4.6.0", "os": "linux", "version": "1.52.0", "date": "2026-06-18T07:20:01.000Z", "distro": "noble", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "7e9d5b94cdcb5e8714d31bca6c8cc823a1e529d9b2a3683463003b8ffd5b7e31", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27743058544" }, { "r": "4.5.3", "os": "mac", "version": "1.52.0", "date": "2026-06-18T07:34:34.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "6006c7925e64f1b14459d2b2ac1508f126f0a292e44c73298e84e14d839850d9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27743058544" }, { "r": "4.6.0", "os": "mac", "version": "1.52.0", "date": "2026-06-18T07:34:05.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "839d0f8b69bd6aea43073908078d25ed999ebaf52190f4640a5d1fa1cdc55d51", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27743058544" }, { "r": "4.6.0", "os": "wasm", "version": "1.52.0", "date": "2026-06-18T07:18:51.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "ec7614f55af2fb940491d837d3366c5db9f1e38b727a18a47722627fe603dba8", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27743058544" }, { "r": "4.7.0", "os": "win", "version": "1.52.0", "date": "2026-06-18T07:18:15.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "18306f0983e293541b982edbc7c74cbbe3d2d9f2980b5a327401461159342353", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27743058544" }, { "r": "4.5.3", "os": "win", "version": "1.52.0", "date": "2026-06-18T07:17:46.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "11b0a8bc93918531e63e233f551c422594a376916f783d96618a86fd3ff18c9d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27743058544" }, { "r": "4.6.0", "os": "win", "version": "1.52.0", "date": "2026-06-18T07:18:06.000Z", "commit": "0011363706a70fbce42289e08a3f0b194f6bb2c0", "fileid": "427a1cf5c030f6a191ced7a5936168f1e86135947f1640d6bd9a7ec72d627103", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27743058544" } ] }