{ "_id": "6a19656dacfb0bcc41de6d35", "Package": "CausalR", "Type": "Package", "Title": "Causal network analysis methods", "Version": "1.45.0", "Date": "2016-11-14", "Author": "Glyn Bradley, Steven Barrett, Chirag Mistry, Mark Pipe, David\nWille, David Riley, Bhushan Bonde, Peter Woollard", "Maintainer": "Glyn Bradley , Steven Barrett\n", "Description": "Causal network analysis methods for regulator prediction\nand network reconstruction from genome scale data.", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, SystemsBiology, Network, GraphAndNetwork,\nNetwork Inference, Transcriptomics, Proteomics,\nDifferentialExpression, RNASeq, Microarray", "License": "GPL (>= 2)", "NeedsCompilation": "no", "RoxygenNote": "5.0.1", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:41:21 UTC", "RemoteUrl": "https://github.com/bioc/CausalR", "RemoteRef": "HEAD", "RemoteSha": "41ac12965fecd7053b08069ccc0986e600dcedb3", "Packaged": { "Date": "2026-05-29 08:25:02 UTC", "User": "root" }, "MD5sum": "4f79c5e2fe8e2c9b45df36c1d7d82f18", "_user": "bioc", "_type": "src", "_file": "CausalR_1.45.0.tar.gz", "_fileid": "a867cb54f835ae52acb3b1c130b485c4d2c2a97ecfc8d260bb850700228ba9f4", "_filesize": 794885, "_sha256": "a867cb54f835ae52acb3b1c130b485c4d2c2a97ecfc8d260bb850700228ba9f4", "_created": "2026-05-29T08:25:02.000Z", "_published": "2026-05-29T10:07:41.735Z", "_jobs": [ { "job": 78465089802, "time": 148, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7286412785" }, { "job": 78465089727, "time": 183, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7286423079" }, { "job": 78465089726, "time": 174, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7286420398" }, { "job": 78465089722, "time": 187, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7288207237" }, { "job": 78465089733, "time": 193, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7288208201" }, { "job": 78464487251, "time": 250, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7286367379" }, { "job": 78465089709, "time": 102, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7286399702" }, { "job": 78465089772, "time": 497, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7286515522" }, { "job": 78465089753, "time": 412, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7286488419" }, { "job": 78465089793, "time": 487, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7286511374" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26626501890", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CausalR", "_commit": { "id": "41ac12965fecd7053b08069ccc0986e600dcedb3", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380081 }, "_maintainer": { "name": "Glyn Bradley", "email": "steven.j.barrett@gsk.com", "login": "glynbradley", "description": "", "uuid": 17427865 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2.0", "role": "Depends" }, { "package": "igraph", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.0", "bioc": "3.24" }, { "branch": "release", "version": "1.44.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "systemsbiology", "network", "graphandnetwork", "network inference", "transcriptomics", "proteomics", "differentialexpression", "rnaseq", "microarray" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 398, "source": "https://www.bioconductor.org/packages/stats/bioc/CausalR" }, "_mentions": 2, "_searchresults": 8, "_rbuild": "4.6.0", "_assets": [ "extra/CausalR.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "AnalysePredictionsList", "CalculateEnrichmentPValue", "CalculateSignificance", "CalculateSignificanceUsingCubicAlgorithm", "CalculateSignificanceUsingCubicAlgorithm1b", "CalculateSignificanceUsingQuarticAlgorithm", "CompareHypothesis", "CreateCCG", "CreateCG", "GetNodeName", "GetNumberOfPositiveAndNegativeEntries", "GetShortestPathsFromCCG", "MakePredictions", "MakePredictionsFromCCG", "MakePredictionsFromCG", "PlotGraphWithNodeNames", "RankTheHypotheses", "ReadExperimentalData", "runSCANR", "ScoreHypothesis", "WriteAllExplainedNodesToSifFile", "WriteExplainedNodesToSifFile" ], "_help": [ { "page": "CausalR-package", "title": "The CausalR package", "concept": [ "CausalR" ], "topics": [ "CausalR-package", "CausalR" ] }, { "page": "AddIDsToVertices", "title": "add IDs to vertices", "topics": [ "AddIDsToVertices" ] }, { "page": "AddWeightsToEdges", "title": "add weights to edges", "topics": [ "AddWeightsToEdges" ] }, { "page": "AnalyseExperimentalData", "title": "analyse experimental data", "topics": [ "AnalyseExperimentalData" ] }, { "page": "AnalysePredictionsList", "title": "analyse predictions list", "concept": [ "CausalR" ], "topics": [ "AnalysePredictionsList" ] }, { "page": "CalculateEnrichmentPValue", "title": "calculates an enrichment p-value", "concept": [ "CausalR" ], "topics": [ "CalculateEnrichmentPValue" ] }, { "page": "CalculateSignificance", "title": "calculate overall significance p-value", "concept": [ "CausalR" ], "topics": [ "CalculateSignificance" ] }, { "page": "CalculateSignificanceUsingCubicAlgorithm", "title": "calculate significance using the cubic algorithm", "concept": [ "CausalR" ], "topics": [ "CalculateSignificanceUsingCubicAlgorithm" ] }, { "page": "CalculateSignificanceUsingCubicAlgorithm1b", "title": "Calculate Significance Using Cubic Algorithm", "concept": [ "CausalR" ], "topics": [ "CalculateSignificanceUsingCubicAlgorithm1b" ] }, { "page": "CalculateSignificanceUsingQuarticAlgorithm", "title": "calculate significance using the quartic algorithm", "concept": [ "CausalR" ], "topics": [ "CalculateSignificanceUsingQuarticAlgorithm" ] }, { "page": "CalculateTotalWeightForAllContingencyTables", "title": "calculate total weight for all contingency tables", "topics": [ "CalculateTotalWeightForAllContingencyTables" ] }, { "page": "CalculateWeightGivenValuesInThreeByThreeContingencyTable", "title": "calculate weight given values in three-by-three contingency table", "topics": [ "CalculateWeightGivenValuesInThreeByThreeContingencyTable" ] }, { "page": "CheckPossibleValuesAreValid", "title": "check possible values are valid", "topics": [ "CheckPossibleValuesAreValid" ] }, { "page": "CheckRowAndColumnSumValuesAreValid", "title": "check row and column sum values are valid", "topics": [ "CheckRowAndColumnSumValuesAreValid" ] }, { "page": "CompareHypothesis", "title": "compare hypothesis", "concept": [ "CausalR" ], "topics": [ "CompareHypothesis" ] }, { "page": "ComputeFinalDistribution", "title": "compute final distribution", "topics": [ "ComputeFinalDistribution" ] }, { "page": "ComputePValueFromDistributionTable", "title": "compute a p-value from the distribution table", "topics": [ "ComputePValueFromDistributionTable" ] }, { "page": "CreateCCG", "title": "create a Computational Causal Graph (CCG)", "concept": [ "CausalR" ], "topics": [ "CreateCCG" ] }, { "page": "CreateCG", "title": "create a Computational Graph (CG)", "concept": [ "CausalR" ], "topics": [ "CreateCG" ] }, { "page": "CreateNetworkFromTable", "title": "create network from table", "topics": [ "CreateNetworkFromTable" ] }, { "page": "DetermineInteractionTypeOfPath", "title": "determine interaction type of path", "topics": [ "DetermineInteractionTypeOfPath" ] }, { "page": "FindApproximateValuesThatWillMaximiseDValue", "title": "find approximate values that will maximise D value", "topics": [ "FindApproximateValuesThatWillMaximiseDValue" ] }, { "page": "FindIdsOfConnectedNodesInSubgraph", "title": "find Ids of connected nodes in subgraph", "topics": [ "FindIdsOfConnectedNodesInSubgraph" ] }, { "page": "FindMaximumDValue", "title": "find maximum D value", "topics": [ "FindMaximumDValue" ] }, { "page": "GetAllPossibleRoundingCombinations", "title": "get score for numbers of correct and incorrect predictions", "topics": [ "GetAllPossibleRoundingCombinations" ] }, { "page": "GetApproximateMaximumDValueFromThreeByTwoContingencyTable", "title": "returns approximate maximum D value or weight for a 3x2 superfamily", "topics": [ "GetApproximateMaximumDValueFromThreeByTwoContingencyTable" ] }, { "page": "GetApproximateMaximumDValueFromTwoByTwoContingencyTable", "title": "computes an approximate maximum D value or weight", "topics": [ "GetApproximateMaximumDValueFromTwoByTwoContingencyTable" ] }, { "page": "GetCombinationsOfCorrectandIncorrectPredictions", "title": "returns table of correct and incorrect predictions", "topics": [ "GetCombinationsOfCorrectandIncorrectPredictions" ] }, { "page": "GetExplainedNodesOfCCG", "title": "Get explained nodes of CCG", "topics": [ "GetExplainedNodesOfCCG" ] }, { "page": "GetInteractionInformation", "title": "returns interaction information from input data", "topics": [ "GetInteractionInformation" ] }, { "page": "GetMatrixOfCausalRelationships", "title": "compute causal relationships matrix", "topics": [ "GetMatrixOfCausalRelationships" ] }, { "page": "GetMaxDValueForAFamily", "title": "get maximun D value for a family", "topics": [ "GetMaxDValueForAFamily" ] }, { "page": "GetMaxDValueForAThreeByTwoFamily", "title": "get maximum D value for three-by-two a family", "topics": [ "GetMaxDValueForAThreeByTwoFamily" ] }, { "page": "GetMaximumDValueFromTwoByTwoContingencyTable", "title": "get maximum D value from two-by-two contingency table", "topics": [ "GetMaximumDValueFromTwoByTwoContingencyTable" ] }, { "page": "GetNodeID", "title": "get CCG node ID", "topics": [ "GetNodeID" ] }, { "page": "GetNodeName", "title": "get node name", "concept": [ "CausalR" ], "topics": [ "GetNodeName" ] }, { "page": "GetNumberOfPositiveAndNegativeEntries", "title": "counts the number of positive and negative entries", "concept": [ "CausalR" ], "topics": [ "GetNumberOfPositiveAndNegativeEntries" ] }, { "page": "GetPathsInSifFormat", "title": "Get paths in Sif format", "topics": [ "GetPathsInSifFormat" ] }, { "page": "GetRegulatedNodes", "title": "get regulated nodes", "topics": [ "GetRegulatedNodes" ] }, { "page": "GetRowAndColumnSumValues", "title": "get row and column sum values", "topics": [ "GetRowAndColumnSumValues" ] }, { "page": "GetScoreForNumbersOfCorrectandIncorrectPredictions", "title": "returns the score for a given number of correct and incorrect predictions", "topics": [ "GetScoreForNumbersOfCorrectandIncorrectPredictions" ] }, { "page": "GetScoresForSingleNode", "title": "Get scores for single node", "topics": [ "GetScoresForSingleNode" ] }, { "page": "GetScoresWeightsMatrix", "title": "get scores weight matrix", "topics": [ "GetScoresWeightsMatrix" ] }, { "page": "GetScoresWeightsMatrixByCubicAlg", "title": "get scores weights matrix by the cubic algorithm", "topics": [ "GetScoresWeightsMatrixByCubicAlg" ] }, { "page": "GetSetOfDifferentiallyExpressedGenes", "title": "get set of differientially expressed genes", "topics": [ "GetSetOfDifferentiallyExpressedGenes" ] }, { "page": "GetSetOfSignificantPredictions", "title": "get set of significant predictions", "topics": [ "GetSetOfSignificantPredictions" ] }, { "page": "GetShortestPathsFromCCG", "title": "get shortest paths from CCG", "concept": [ "CausalR" ], "topics": [ "GetShortestPathsFromCCG" ] }, { "page": "GetWeightForNumbersOfCorrectandIncorrectPredictions", "title": "get weight for numbers of correct and incorrect predictions", "topics": [ "GetWeightForNumbersOfCorrectandIncorrectPredictions" ] }, { "page": "GetWeightsAboveHypothesisScoreAndTotalWeights", "title": "get weights above hypothesis score and total weights", "topics": [ "GetWeightsAboveHypothesisScoreAndTotalWeights" ] }, { "page": "GetWeightsAboveHypothesisScoreForAThreeByTwoTable", "title": "updates weights for contingency table and produce values for p-value calculation", "topics": [ "GetWeightsAboveHypothesisScoreForAThreeByTwoTable" ] }, { "page": "GetWeightsFromInteractionInformation", "title": "get weights from interaction information", "topics": [ "GetWeightsFromInteractionInformation" ] }, { "page": "MakePredictions", "title": "make predictions", "concept": [ "CausalR" ], "topics": [ "MakePredictions" ] }, { "page": "MakePredictionsFromCCG", "title": "make predictions from CCG", "concept": [ "CausalR" ], "topics": [ "MakePredictionsFromCCG" ] }, { "page": "MakePredictionsFromCG", "title": "make predictions from CG", "concept": [ "CausalR" ], "topics": [ "MakePredictionsFromCG" ] }, { "page": "OrderHypotheses", "title": "order hypotheses", "topics": [ "OrderHypotheses" ] }, { "page": "PlotGraphWithNodeNames", "title": "plot graph with node names", "concept": [ "CausalR" ], "topics": [ "PlotGraphWithNodeNames" ] }, { "page": "PopulateTheThreeByThreeContingencyTable", "title": "populate the three-by-three contingency table", "topics": [ "PopulateTheThreeByThreeContingencyTable" ] }, { "page": "PopulateTwoByTwoContingencyTable", "title": "Populate Two by Two Contingency Table", "topics": [ "PopulateTwoByTwoContingencyTable" ] }, { "page": "ProcessExperimentalData", "title": "process experimental data", "topics": [ "ProcessExperimentalData" ] }, { "page": "RankTheHypotheses", "title": "rank the hypotheses", "concept": [ "CausalR" ], "topics": [ "RankTheHypotheses" ] }, { "page": "ReadExperimentalData", "title": "read experimental data", "concept": [ "CausalR" ], "topics": [ "ReadExperimentalData" ] }, { "page": "ReadSifFileToTable", "title": "read .sif to Table", "topics": [ "ReadSifFileToTable" ] }, { "page": "RemoveIDsNotInExperimentalData", "title": "remove IDs not in experimental data", "topics": [ "RemoveIDsNotInExperimentalData" ] }, { "page": "runRankHypothesis", "title": "run rank the hypothesis", "topics": [ "runRankHypothesis" ] }, { "page": "runSCANR", "title": "run ScanR", "concept": [ "CausalR" ], "topics": [ "runSCANR" ] }, { "page": "ScoreHypothesis", "title": "score hypothesis", "concept": [ "CausalR" ], "topics": [ "ScoreHypothesis" ] }, { "page": "ValidateFormatOfDataTable", "title": "validate format of the experimental data table", "topics": [ "ValidateFormatOfDataTable" ] }, { "page": "ValidateFormatOfTable", "title": "validate format of table", "topics": [ "ValidateFormatOfTable" ] }, { "page": "WriteAllExplainedNodesToSifFile", "title": "Write all explained nodes to Sif file", "concept": [ "CausalR" ], "topics": [ "WriteAllExplainedNodesToSifFile" ] }, { "page": "WriteExplainedNodesToSifFile", "title": "Write explained nodes to Sif file", "concept": [ "CausalR" ], "topics": [ "WriteExplainedNodesToSifFile" ] } ], "_rundeps": [ "cli", "cpp11", "glue", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "rlang", "vctrs" ], "_vignettes": [ { "source": "CausalR.rnw", "filename": "CausalR.pdf", "title": "CausalR : an R Package for causal reasoning on networks", "engine": "knitr::knitr", "headings": [], "created": "2016-11-16 14:54:56", "modified": "2016-11-16 14:54:56", "commits": 1 } ], "_score": 3.6020599913279625, "_indexed": true, "_nocasepkg": "causalr", "_universes": [ "bioc", "glynbradley" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.45.0", "date": "2026-05-29T08:28:02.000Z", "distro": "noble", "commit": "41ac12965fecd7053b08069ccc0986e600dcedb3", "fileid": "5d014a2d94c73037d47399e2d705bba46a79fb5a5064e9df87853f3c58035db7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626501890" }, { "r": "4.6.0", "os": "linux", "version": "1.45.0", "date": "2026-05-29T08:27:54.000Z", "distro": "noble", "commit": "41ac12965fecd7053b08069ccc0986e600dcedb3", "fileid": "d8fc862f5212ceb8ca97d5633c5252748d6f7935d46656b31b8e6d393f156fa5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626501890" }, { "r": "4.5.3", "os": "mac", "version": "1.45.0", "date": "2026-05-29T10:07:07.000Z", "commit": "41ac12965fecd7053b08069ccc0986e600dcedb3", "fileid": "c02e062d07a8a2d523d1f4ca1499a172cfa0e8e35c34b7a7a8075f401eac9f2c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626501890" }, { "r": "4.6.0", "os": "mac", "version": "1.45.0", "date": "2026-05-29T10:07:08.000Z", "commit": "41ac12965fecd7053b08069ccc0986e600dcedb3", "fileid": "cc920c03b5ab405d4f50d30f57a6115e80d55e5007eed04b0b65beb1f0f5b32c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626501890" }, { "r": "4.6.0", "os": "wasm", "version": "1.45.0", "date": "2026-05-29T08:27:00.000Z", "commit": "41ac12965fecd7053b08069ccc0986e600dcedb3", "fileid": "66d91901c23ea1f456f7af0e7472aa2562b76aab5cc46f74d3778faa6f4c6c3f", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626501890" }, { "r": "4.7.0", "os": "win", "version": "1.45.0", "date": "2026-05-29T08:33:04.000Z", "commit": "41ac12965fecd7053b08069ccc0986e600dcedb3", "fileid": "6562fc42f7b7154a45fa8357ef613ed2db51a4440ac72d6584f83030489f1154", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626501890" }, { "r": "4.5.3", "os": "win", "version": "1.45.0", "date": "2026-05-29T08:31:32.000Z", "commit": "41ac12965fecd7053b08069ccc0986e600dcedb3", "fileid": "3540987ac48c6ec885f353373ca84999a1469bc1bb1a07540898889a10eabb9a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626501890" }, { "r": "4.6.0", "os": "win", "version": "1.45.0", "date": "2026-05-29T08:32:48.000Z", "commit": "41ac12965fecd7053b08069ccc0986e600dcedb3", "fileid": "a00d9df650c19368af9bf4dca8d5d893342247aa32cedcdae83154dd5ccf3ce7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626501890" } ] }