{
  "_id": "6a1ac3681d7bb097a09da555",
  "Package": "MOSClip",
  "Title": "Multi Omics Survival Clip",
  "Version": "1.7.0",
  "Authors@R": "c(\nperson(given = \"Paolo\", family = \"Martini\", role = c(\"aut\", \"cre\"),\nemail = \"paolo.martini@unibs.it\",\ncomment = c(ORCID = \"0000-0002-0146-1031\")),\nperson(given = \"Anna\", family = \"Bortolato\", role = c(\"aut\"),\nemail = \"anna.bortolato@unipd.it\",\ncomment = c(ORCID = \"0009-0009-9327-6084\")),\nperson(given = \"Anna\", family = \"Tanada\", role = c(\"aut\"),\nemail = \"annacarolinaemi.delimatanada@phd.unipd.it\",\ncomment = c(ORCID = \"0000-0003-3224-0538\")),\nperson(given = \"Enrica\", family = \"Calura\", role = c(\"aut\"),\nemail = \"enrica.calura@unipd.it\",\ncomment = c(ORCID = \"0000-0001-8463-2432\")),\nperson(given = \"Stefania\", family = \"Pirrotta\", role = c(\"aut\"),\nemail = \"stefania.pirrotta@phd.unipd.it\",\ncomment = c(ORCID = \"0009-0004-0030-217X\")),\nperson(given = \"Federico\", family = \"Agostinis\", role = c(\"aut\"),\nemail = \"federico.agostinis@outlook.com\")\n)",
  "Description": "Topological pathway analysis tool able to integrate\nmulti-omics data. It finds survival-associated modules or\nsignificant modules for two-class analysis. This tool have two\nmain methods: pathway tests and module tests. The latter method\nallows the user to dig inside the pathways itself.",
  "License": "AGPL-3",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "biocViews": "Software, StatisticalMethod, GraphAndNetwork, Survival,\nRegression, DimensionReduction, Pathways, Reactome",
  "BugReports": "https://github.com/CaluraLab/MOSClip/issues",
  "URL": "https://github.com/CaluraLab/MOSClip/",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev perl xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:03:58 UTC",
  "RemoteUrl": "https://github.com/bioc/MOSClip",
  "RemoteRef": "HEAD",
  "RemoteSha": "ab63e189fdf1f41cb76b9d15e5a12cba12455757",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:38:09 UTC",
    "User": "root"
  },
  "Author": "Paolo Martini [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-0146-1031>),\nAnna Bortolato [aut] (ORCID: <https://orcid.org/0009-0009-9327-6084>),\nAnna Tanada [aut] (ORCID: <https://orcid.org/0000-0003-3224-0538>),\nEnrica Calura [aut] (ORCID: <https://orcid.org/0000-0001-8463-2432>),\nStefania Pirrotta [aut] (ORCID:\n<https://orcid.org/0009-0004-0030-217X>),\nFederico Agostinis [aut]",
  "Maintainer": "Paolo Martini <paolo.martini@unibs.it>",
  "MD5sum": "4f400016a26957bf457e3d83ed162d31",
  "_user": "bioc",
  "_type": "src",
  "_file": "MOSClip_1.7.0.tar.gz",
  "_fileid": "ae08fc0036bcc304ff95fcb87f0458a486d3fec0df125609fb5d12b1c13cdc84",
  "_filesize": 2239066,
  "_sha256": "ae08fc0036bcc304ff95fcb87f0458a486d3fec0df125609fb5d12b1c13cdc84",
  "_created": "2026-05-30T07:38:09.000Z",
  "_published": "2026-05-30T11:00:56.386Z",
  "_jobs": [
    {
      "job": 78634104005,
      "time": 275,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306567390"
    },
    {
      "job": 78634103991,
      "time": 641,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306602723"
    },
    {
      "job": 78634103998,
      "time": 653,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306603991"
    },
    {
      "job": 78634103989,
      "time": 350,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307683142"
    },
    {
      "job": 78634103997,
      "time": 422,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307690383"
    },
    {
      "job": 78633736581,
      "time": 434,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306539496"
    },
    {
      "job": 78634103988,
      "time": 241,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306563766"
    },
    {
      "job": 78634104012,
      "time": 930,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306630862"
    },
    {
      "job": 78634104011,
      "time": 800,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306618580"
    },
    {
      "job": 78634104009,
      "time": 517,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306590862"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 5
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678151551",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/MOSClip",
  "_commit": {
    "id": "ab63e189fdf1f41cb76b9d15e5a12cba12455757",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381438
  },
  "_maintainer": {
    "name": "Paolo Martini",
    "email": "paolo.martini@unibs.it",
    "orcid": "0000-0002-0146-1031"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "MultiAssayExperiment",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "survminer",
      "role": "Imports"
    },
    {
      "package": "graph",
      "role": "Imports"
    },
    {
      "package": "graphite",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "checkmate",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "SuperExactTest",
      "role": "Imports"
    },
    {
      "package": "reshape",
      "role": "Imports"
    },
    {
      "package": "NbClust",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "FactoMineR",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "corpcor",
      "role": "Imports"
    },
    {
      "package": "coxrobust",
      "role": "Imports"
    },
    {
      "package": "elasticnet",
      "role": "Imports"
    },
    {
      "package": "gRbase",
      "role": "Imports"
    },
    {
      "package": "ggplotify",
      "role": "Imports"
    },
    {
      "package": "qpgraph",
      "role": "Imports"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "MASS",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "EDASeq",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-39",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.7.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.6.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "statisticalmethod",
    "graphandnetwork",
    "survival",
    "regression",
    "dimensionreduction",
    "pathways",
    "reactome"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "annabortolato",
      "count": 211,
      "uuid": 181740678
    },
    {
      "user": "cavei",
      "count": 13,
      "uuid": 20298062
    },
    {
      "user": "spirrotta",
      "count": 12,
      "uuid": 107050220
    },
    {
      "user": "jwokaty",
      "count": 3,
      "uuid": 1744257
    },
    {
      "user": "annatanada",
      "count": 2,
      "uuid": 157597479
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 234,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MOSClip"
  },
  "_devurl": "https://github.com/caluralab/mosclip",
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MOSClip.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/caluralab/mosclip",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addResamplingCounts",
    "annotePathwayToFather",
    "availableOmicMethods",
    "computeFreqs",
    "computeOmicsIntersections",
    "downloadPathwayRelationFromReactome",
    "getPathwaysModulesSuccess",
    "makeOmics",
    "multiOmicsSurvivalModuleTest",
    "multiOmicsSurvivalPathwayTest",
    "multiOmicsTwoClassModuleTest",
    "multiOmicsTwoClassPathwayTest",
    "multiPathwayModuleReport",
    "multiPathwayReport",
    "plotFrequencies",
    "plotModuleHeat",
    "plotModuleInGraph",
    "plotModuleKM",
    "plotModuleReport",
    "plotMultiPathwayReport",
    "plotPathwayHeat",
    "plotPathwayKM",
    "resamplingModulesSurvival",
    "resamplingModulesTwoClass",
    "resamplingPathwaySurvival",
    "resamplingPathwayTwoClass",
    "runSupertest",
    "selectStablePathwaysModules",
    "showModule",
    "showMOSpalette",
    "showOmics",
    "showPathway",
    "stripModulesFromPathways"
  ],
  "_datasets": [
    {
      "name": "multiOmics",
      "title": "Omics class object with TCGA ovarian data",
      "object": "multiOmics",
      "file": "multiOmics.rda",
      "class": [
        "Omics"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "multiOmicsTopo",
      "title": "Omics class object with TCGA ovarian data for topological analysis",
      "object": "multiOmicsTopo",
      "file": "multiOmicsTopo.rda",
      "class": [
        "Omics"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ovarianDataset",
      "title": "ExperimentList class object with TCGA ovarian data",
      "object": "ovarianDataset",
      "file": "ovarianDataset.rda",
      "class": [
        "ExperimentList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "reactSmall",
      "title": "PathwayList of pathways from Reactome",
      "object": "reactSmall",
      "file": "reactSmall.rda",
      "class": [
        "PathwayList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "annotePathwayToFather",
      "title": "Find Pathway Fathers",
      "topics": [
        "annotePathwayToFather"
      ]
    },
    {
      "page": "availableOmicMethods",
      "title": "Get available Omics Summarizing Methods",
      "topics": [
        "availableOmicMethods"
      ]
    },
    {
      "page": "resampling",
      "title": "Check if all the list object have the same order of pathway module",
      "topics": [
        "checkOrder",
        "filterExpr",
        "filterMultiOmicsForSamples",
        "mergeCol",
        "preparePerms",
        "resolveAndOrder"
      ]
    },
    {
      "page": "compPCs",
      "title": "Regular PCA",
      "topics": [
        "compPCs"
      ]
    },
    {
      "page": "computeFreqs",
      "title": "Compute Frequencies in a Named List",
      "topics": [
        "computeFreqs"
      ]
    },
    {
      "page": "computeOmicsIntersections",
      "title": "Compute Omics Intersections",
      "topics": [
        "computeOmicsIntersections"
      ]
    },
    {
      "page": "computePCs",
      "title": "compute PCs.",
      "topics": [
        "computePCs"
      ]
    },
    {
      "page": "convertPathway",
      "title": "A generic function to convert pathway",
      "topics": [
        "convertPathway"
      ]
    },
    {
      "page": "createCoxObj",
      "title": "Create Cox Object",
      "topics": [
        "createCoxObj"
      ]
    },
    {
      "page": "createDataModule",
      "title": "Create Data Module",
      "topics": [
        "createDataModule"
      ]
    },
    {
      "page": "createMOMView",
      "title": "Create the list of covariates that are going to be tested",
      "topics": [
        "createMOMView"
      ]
    },
    {
      "page": "downloadPathwayRelationFromReactome",
      "title": "Download Reactome Pathway Relations",
      "topics": [
        "downloadPathwayRelationFromReactome"
      ]
    },
    {
      "page": "estimateExprCov",
      "title": "Estimate Single Covariance Matrix",
      "topics": [
        "estimateExprCov"
      ]
    },
    {
      "page": "graph-processing",
      "title": "Extract the maximal cliques",
      "topics": [
        "extractCliquesFromDag",
        "mmmoralize"
      ]
    },
    {
      "page": "extractSummaryFromBinary",
      "title": "Extract Summary Binary from MultiOmics Objects",
      "topics": [
        "extractSummaryFromBinary"
      ]
    },
    {
      "page": "extractSummaryFromCluster",
      "title": "Extract Summary Cluster from MultiOmics Objects",
      "topics": [
        "extractSummaryFromCluster"
      ]
    },
    {
      "page": "extractSummaryFromNumberOfEvents",
      "title": "Extract Summary Binary from MultiOmics Objects",
      "topics": [
        "extractSummaryFromNumberOfEvents"
      ]
    },
    {
      "page": "extractSummaryFromPCA",
      "title": "Extract Summary PCA from MultiOmics Objects",
      "topics": [
        "extractSummaryFromPCA"
      ]
    },
    {
      "page": "getPathFathers",
      "title": "Retrieves pathways relatives",
      "topics": [
        "getPathFathers"
      ]
    },
    {
      "page": "glmTest",
      "title": "Two-classes glm test.",
      "topics": [
        "glmTest"
      ]
    },
    {
      "page": "guessInvolvement",
      "title": "Guess the most influent features from MultiOmics Survival or Two-class results.",
      "topics": [
        "guessInvolvement"
      ]
    },
    {
      "page": "guessInvolvementPathway",
      "title": "Guess the most influent features from MultiOmics Survival or Two-class results.",
      "topics": [
        "guessInvolvementPathway"
      ]
    },
    {
      "page": "id2name",
      "title": "Convert id to pathway name",
      "topics": [
        "id2name"
      ]
    },
    {
      "page": "makeOmics",
      "title": "Omics class initializer function",
      "topics": [
        "makeOmics"
      ]
    },
    {
      "page": "makePositiveDefinite",
      "title": "Make positive and definite covariance matrix",
      "topics": [
        "makePositiveDefinite"
      ]
    },
    {
      "page": "mapPathwaysIDfromGraphite",
      "title": "Map Pathways ID from Graphite",
      "topics": [
        "mapPathwaysIDfromGraphite"
      ]
    },
    {
      "page": "minOrNA",
      "title": "Minimum or NA",
      "topics": [
        "minOrNA"
      ]
    },
    {
      "page": "MOSClip",
      "title": "MOSClip: Multi-Omics Survival Clip",
      "topics": [
        "MOSClip-package",
        "MOSClip"
      ]
    },
    {
      "page": "multiOmics",
      "title": "Omics class object with TCGA ovarian data",
      "topics": [
        "multiOmics"
      ]
    },
    {
      "page": "MultiOmicsModules-class",
      "title": "Multi Omics Modules.",
      "topics": [
        "MultiOmicsModules-class",
        "showModule,MultiOmicsModules-method"
      ]
    },
    {
      "page": "MultiOmicsPathway-class",
      "title": "Multi Omics Pathway.",
      "topics": [
        "MultiOmicsPathway-class",
        "showPathway,MultiOmicsPathway-method"
      ]
    },
    {
      "page": "multiOmicsSurvivalModuleTest",
      "title": "Compute Multi Omics Survival in Pathway Modules",
      "topics": [
        "multiOmicsSurvivalModuleTest"
      ]
    },
    {
      "page": "multiOmicsSurvivalPathwayTest",
      "title": "Compute Multi Omics Survival in Pathways",
      "topics": [
        "multiOmicsSurvivalPathwayTest"
      ]
    },
    {
      "page": "multiOmicsTopo",
      "title": "Omics class object with TCGA ovarian data for topological analysis",
      "topics": [
        "multiOmicsTopo"
      ]
    },
    {
      "page": "multiOmicsTwoClassModuleTest",
      "title": "Computes Multi Omics Two-Class in Pathway Modules",
      "topics": [
        "multiOmicsTwoClassModuleTest"
      ]
    },
    {
      "page": "multiOmicsTwoClassPathwayTest",
      "title": "Compute Multi Omics Two-Class in Pathways",
      "topics": [
        "multiOmicsTwoClassPathwayTest"
      ]
    },
    {
      "page": "multiPathwayModuleReport",
      "title": "Provides a Table of the Modules Test Results",
      "topics": [
        "multiPathwayModuleReport"
      ]
    },
    {
      "page": "multiPathwayReport",
      "title": "Summarize pathways' info from a list of MultiOmicsPathway objects (MOP)",
      "topics": [
        "multiPathwayReport"
      ]
    },
    {
      "page": "Omics-class",
      "title": "Omics.",
      "topics": [
        "Omics",
        "Omics-class",
        "showOmics,Omics-method"
      ]
    },
    {
      "page": "ovarianDataset",
      "title": "ExperimentList class object with TCGA ovarian data",
      "topics": [
        "ovarianDataset"
      ]
    },
    {
      "page": "plotFrequencies",
      "title": "Plot Frequencies of Pathway Fathers for Omics intersection",
      "topics": [
        "plotFrequencies"
      ]
    },
    {
      "page": "plotModuleHeat",
      "title": "Plot a Heatmap of a Module by Omics",
      "topics": [
        "plotModuleHeat"
      ]
    },
    {
      "page": "plotModuleInGraph",
      "title": "Plot a Directed Graph of the MultiOmicsModules Object",
      "topics": [
        "plotModuleInGraph"
      ]
    },
    {
      "page": "plotModuleKM",
      "title": "Plot Kaplan-Meier survival curves of a specific module",
      "topics": [
        "plotModuleKM"
      ]
    },
    {
      "page": "plotModuleReport",
      "title": "Plot a table of a 'MultiOmicsModules' (MOM) object",
      "topics": [
        "plotModuleReport"
      ]
    },
    {
      "page": "plotMultiPathwayReport",
      "title": "Summarize and plot pathways' info from a list of 'MultiOmicsPathway' (MOP)",
      "topics": [
        "plotMultiPathwayReport"
      ]
    },
    {
      "page": "plotPathwayHeat",
      "title": "Plot heatmaps of the pathway by omics",
      "topics": [
        "plotPathwayHeat"
      ]
    },
    {
      "page": "plotPathwayKM",
      "title": "Plot Kaplan-Meier survival curves of a specific pathway",
      "topics": [
        "plotPathwayKM"
      ]
    },
    {
      "page": "pvalueSummary",
      "title": "Compute pvalue Summary",
      "topics": [
        "pvalueSummary"
      ]
    },
    {
      "page": "reactSmall",
      "title": "PathwayList of pathways from Reactome",
      "topics": [
        "reactSmall"
      ]
    },
    {
      "page": "removeSelfLoops",
      "title": "Remove self loops from a graphNEL",
      "topics": [
        "removeSelfLoops"
      ]
    },
    {
      "page": "resampling-Survival",
      "title": "Resampling function for survival analysis on modules",
      "topics": [
        "resamplingModulesSurvival",
        "resamplingPathwaySurvival"
      ]
    },
    {
      "page": "resampling-TwoClass",
      "title": "Resampling function for two-class analysis on modules",
      "topics": [
        "resamplingModulesTwoClass",
        "resamplingPathwayTwoClass"
      ]
    },
    {
      "page": "runSupertest",
      "title": "Performs a Exact test - analysis of omics intersection",
      "topics": [
        "runSupertest"
      ]
    },
    {
      "page": "evaluateResampling",
      "title": "Select stable pathway modules",
      "topics": [
        "addResamplingCounts",
        "getPathwaysModulesSuccess",
        "selectStablePathwaysModules"
      ]
    },
    {
      "page": "showModule",
      "title": "A generic function showing pathway's module info",
      "topics": [
        "showModule"
      ]
    },
    {
      "page": "showMOSpalette",
      "title": "Shows the MOSClip palette.",
      "topics": [
        "showMOSpalette"
      ]
    },
    {
      "page": "showOmics",
      "title": "A generic functions showing parameter associated with each omics",
      "topics": [
        "showOmics"
      ]
    },
    {
      "page": "showPathway",
      "title": "A generic function showing pathway info",
      "topics": [
        "showPathway"
      ]
    },
    {
      "page": "sparseCompPCs",
      "title": "Sparse PCA",
      "topics": [
        "sparseCompPCs"
      ]
    },
    {
      "page": "stripModulesFromPathways",
      "title": "Remove Module Number From Pathway Name",
      "topics": [
        "stripModulesFromPathways"
      ]
    },
    {
      "page": "summarizeInCluster",
      "title": "Summarize Using Cluster Analysis",
      "topics": [
        "summarizeInCluster"
      ]
    },
    {
      "page": "summarizeOmicsResByMinPvalue",
      "title": "Summarize Omics Covaraites By Min Pvalue",
      "topics": [
        "summarizeOmicsResByMinPvalue"
      ]
    },
    {
      "page": "summarizeToBinaryDirectionalEvents",
      "title": "Summarize To Binary Directional Events",
      "topics": [
        "summarizeToBinaryDirectionalEvents"
      ]
    },
    {
      "page": "summarizeToBinaryEvents",
      "title": "Summarize To Binary Events",
      "topics": [
        "summarizeToBinaryEvents"
      ]
    },
    {
      "page": "summarizeToNumberOfDirectionalEvents",
      "title": "Summarize With Directed Sum",
      "topics": [
        "summarizeToNumberOfDirectionalEvents"
      ]
    },
    {
      "page": "summarizeToNumberOfEvents",
      "title": "Summarize To Number of Binary Events",
      "topics": [
        "summarizeToNumberOfEvents"
      ]
    },
    {
      "page": "summarizeWithPca",
      "title": "Summarize Using PCA",
      "topics": [
        "summarizeWithPca"
      ]
    },
    {
      "page": "survivalcox",
      "title": "Cox Model Analysis",
      "topics": [
        "survivalcox"
      ]
    },
    {
      "page": "survivalcoxr",
      "title": "Cox Robust Model Analysis",
      "topics": [
        "coxrsummary",
        "survivalcoxr"
      ]
    },
    {
      "page": "topoCompPCs",
      "title": "Topological PCA",
      "topics": [
        "topoCompPCs"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/MOSClip/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "car",
    "carData",
    "checkmate",
    "cigarillo",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "commonmark",
    "ComplexHeatmap",
    "corpcor",
    "corrplot",
    "cowplot",
    "coxrobust",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "DBI",
    "DelayedArray",
    "Deriv",
    "digest",
    "dir.expiry",
    "doBy",
    "doParallel",
    "dplyr",
    "DT",
    "elasticnet",
    "ellipse",
    "emmeans",
    "estimability",
    "evaluate",
    "exactRankTests",
    "FactoMineR",
    "farver",
    "fastmap",
    "filelock",
    "flashClust",
    "fontawesome",
    "foreach",
    "forecast",
    "formatR",
    "Formula",
    "fracdiff",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GetoptLong",
    "ggplot2",
    "ggplotify",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "ggtext",
    "GlobalOptions",
    "glue",
    "graph",
    "graphite",
    "gRbase",
    "gridExtra",
    "gridGraphics",
    "gridtext",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "igraph",
    "IRanges",
    "isoband",
    "iterators",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "lars",
    "later",
    "lattice",
    "lazyeval",
    "leaps",
    "lifecycle",
    "litedown",
    "lme4",
    "lmtest",
    "magrittr",
    "markdown",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "maxstat",
    "memoise",
    "mgcv",
    "microbenchmark",
    "mime",
    "minqa",
    "modelr",
    "multcompView",
    "MultiAssayExperiment",
    "mvtnorm",
    "NbClust",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "org.Hs.eg.db",
    "otel",
    "pbkrtest",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "polynom",
    "promises",
    "purrr",
    "qpgraph",
    "qtl",
    "quantreg",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RCurl",
    "Rdpack",
    "reformulas",
    "reshape",
    "restfulr",
    "Rgraphviz",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "Rsamtools",
    "RSQLite",
    "rstatix",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterplot3d",
    "Seqinfo",
    "shape",
    "snow",
    "SparseArray",
    "SparseM",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "SuperExactTest",
    "survival",
    "survminer",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tinytex",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml",
    "yulab.utils",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "mosclip_vignette.Rmd",
      "filename": "mosclip_vignette.html",
      "title": "MOSClip vignette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Abstract",
        "Introduction",
        "Installation",
        "How to use MOSClip for survival analysis",
        "Module analysis",
        "Graphical exploration of MOSClip module results",
        "Pathway analysis",
        "Graphical exploration of MOSClip pathway results",
        "Additional functionalities",
        "Session Information",
        "References"
      ],
      "created": "2024-09-16 13:36:10",
      "modified": "2024-10-15 16:14:14",
      "commits": 4
    }
  ],
  "_score": 4.778151250383644,
  "_indexed": true,
  "_nocasepkg": "mosclip",
  "_universes": [
    "bioc",
    "caluralab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-05-30T07:44:04.000Z",
      "distro": "noble",
      "commit": "ab63e189fdf1f41cb76b9d15e5a12cba12455757",
      "fileid": "4455592a78ac5ae3208d1f02349d07f9fe7956db2524ae4a53a18cc50849c152",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678151551"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-05-30T07:43:53.000Z",
      "distro": "noble",
      "commit": "ab63e189fdf1f41cb76b9d15e5a12cba12455757",
      "fileid": "17277cddb64aba2d193dc05419faf61afe9b478d76e1cce2a60e6d4db27b9d71",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678151551"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-05-30T10:53:27.000Z",
      "commit": "ab63e189fdf1f41cb76b9d15e5a12cba12455757",
      "fileid": "6632217bc9369df8feb862f656dbdf02e3a75370346b604d19b5a1d4bcdc8f0c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678151551"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-05-30T10:54:15.000Z",
      "commit": "ab63e189fdf1f41cb76b9d15e5a12cba12455757",
      "fileid": "934fccae007123888129683256fdd8a505ab6f5b565a98dbbf0be476a104e2b7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678151551"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.7.0",
      "date": "2026-05-30T07:43:15.000Z",
      "commit": "ab63e189fdf1f41cb76b9d15e5a12cba12455757",
      "fileid": "06e182da02fcac8abb6729337bfbe5382192198f4411fb76278b850afdef1ac4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678151551"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-05-30T07:47:36.000Z",
      "commit": "ab63e189fdf1f41cb76b9d15e5a12cba12455757",
      "fileid": "f4609f64c22e014eb628611f125b9d023eaa7b685b559f8e6a04f36b70a818b1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678151551"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-05-30T07:46:38.000Z",
      "commit": "ab63e189fdf1f41cb76b9d15e5a12cba12455757",
      "fileid": "ba6100a38a6d501757b56e754ca36c712bc0e9c26e52d755b01fbd90e739073d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678151551"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-05-30T07:41:52.000Z",
      "commit": "ab63e189fdf1f41cb76b9d15e5a12cba12455757",
      "fileid": "91befd247fa0432cf377ce261d5af032969cf6c812ce6108ab0f9bb5d74d9fe5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678151551"
    }
  ]
}