{
  "_id": "6a1bdca71d7bb097a0a174ab",
  "Package": "CHRONOS",
  "Version": "1.40.0",
  "Date": "2020-09-05",
  "Title": "CHRONOS: A time-varying method for microRNA-mediated sub-pathway\nenrichment analysis",
  "Author": "Aristidis G. Vrahatis, Konstantina Dimitrakopoulou, Panos\nBalomenos",
  "Maintainer": "Panos Balomenos <balomenos@upatras.gr>",
  "Description": "A package used for efficient unraveling of the inherent\ndynamic properties of pathways. MicroRNA-mediated subpathway\ntopologies are extracted and evaluated by exploiting the\ntemporal transition and the fold change activity of the linked\ngenes/microRNAs.",
  "SystemRequirements": "Java version >= 1.7, Pandoc",
  "License": "GPL-2",
  "NeedsCompilation": "no",
  "LazyLoad": "yes",
  "VignetteBuilder": "knitr",
  "biocViews": "SystemsBiology, GraphAndNetwork, Pathways, KEGG",
  "Config/pak/sysreqs": "libglpk-dev make default-jdk libicu-dev libpng-dev\nlibxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:29 UTC",
  "RemoteUrl": "https://github.com/bioc/CHRONOS",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "ae77439d0da121b5bceff02322475497b55ace4c",
  "Packaged": {
    "Date": "2026-05-31 06:30:15 UTC",
    "User": "root"
  },
  "MD5sum": "9f6f50e40ec2eb9422b093c515378242",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "CHRONOS_1.40.0.tar.gz",
  "_fileid": "5f0760d75146690672f318254eabbce97eb26365a2fb1be4af67f20a002d2a0c",
  "_filesize": 1158258,
  "_sha256": "5f0760d75146690672f318254eabbce97eb26365a2fb1be4af67f20a002d2a0c",
  "_created": "2026-05-31T06:30:15.000Z",
  "_published": "2026-05-31T07:00:55.744Z",
  "_jobs": [
    {
      "job": 78705666105,
      "time": 192,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7314458334"
    },
    {
      "job": 78705666100,
      "time": 307,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7314471320"
    },
    {
      "job": 78705666098,
      "time": 308,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7314471451"
    },
    {
      "job": 78705666101,
      "time": 358,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7314617888"
    },
    {
      "job": 78705666099,
      "time": 406,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7314622321"
    },
    {
      "job": 78705438536,
      "time": 253,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314436728"
    },
    {
      "job": 78705666102,
      "time": 152,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314453972"
    },
    {
      "job": 78705666110,
      "time": 516,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7314495643"
    },
    {
      "job": 78705666144,
      "time": 604,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7314505689"
    },
    {
      "job": 78705666114,
      "time": 229,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7314462319"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705336171",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/CHRONOS",
  "_commit": {
    "id": "ae77439d0da121b5bceff02322475497b55ace4c",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380209
  },
  "_maintainer": {
    "name": "Panos Balomenos",
    "email": "balomenos@upatras.gr",
    "login": "balomenos",
    "description": "",
    "uuid": 17261772
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "XML",
      "role": "Imports"
    },
    {
      "package": "RCurl",
      "role": "Imports"
    },
    {
      "package": "RBGL",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "openxlsx",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "graph",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "biomaRt",
      "role": "Imports"
    },
    {
      "package": "rJava",
      "role": "Imports"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "systemsbiology",
    "graphandnetwork",
    "pathways",
    "kegg",
    "openjdk"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 390,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CHRONOS"
  },
  "_mentions": 3,
  "_searchresults": 13,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/CHRONOS.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "CHRONOSrun",
    "convertMiRNANomenclature",
    "convertNomenclature",
    "createPathwayGraphs",
    "downloadKEGGPathwayList",
    "downloadMiRecords",
    "downloadPathways",
    "extractLinearSubpathways",
    "extractNonLinearSubpathways",
    "getEdgeTypes",
    "importExpressions",
    "pathwayMeasures",
    "scoreSubpathways",
    "subpathwayKEGGmap",
    "subpathwayMiRNAs",
    "visualizeResults"
  ],
  "_help": [
    {
      "page": "CHRONOSrun",
      "title": "Default run of CHRONOS",
      "topics": [
        "CHRONOSrun"
      ]
    },
    {
      "page": "convertMiRNANomenclature",
      "title": "Conform miRNA annotations to the ones currently used by miRecords.",
      "topics": [
        "convertMiRNANomenclature"
      ]
    },
    {
      "page": "convertNomenclature",
      "title": "Convert genes identifier nomenclature.",
      "topics": [
        "convertNomenclature"
      ]
    },
    {
      "page": "createPathwayGraphs",
      "title": "Convert KEGG Pathways to Gene-Gene Network Graphs.",
      "topics": [
        "createPathwayGraphs"
      ]
    },
    {
      "page": "downloadKEGGPathwayList",
      "title": "Retrieve all availiable pathways for an organism.",
      "topics": [
        "downloadKEGGPathwayList"
      ]
    },
    {
      "page": "downloadMiRecords",
      "title": "Download miRNA-mRNA interactions for an organism.",
      "topics": [
        "downloadMiRecords"
      ]
    },
    {
      "page": "downloadPathways",
      "title": "Download KEGG pathways in KGML format.",
      "topics": [
        "downloadPathways"
      ]
    },
    {
      "page": "extractLinearSubpathways",
      "title": "Linear subpathway extraction from pathway graphs",
      "topics": [
        "extractLinearSubpathways"
      ]
    },
    {
      "page": "extractNonLinearSubpathways",
      "title": "Non linear subpathway extraction from pathway graphs",
      "topics": [
        "extractNonLinearSubpathways"
      ]
    },
    {
      "page": "getEdgeTypes",
      "title": "Map various types of gene-gene interactions in KGML files to edge types in corresponding pathway graphs.",
      "topics": [
        "getEdgeTypes"
      ]
    },
    {
      "page": "importExpressions",
      "title": "Import gene and miRNA expressions from",
      "topics": [
        "importExpressions"
      ]
    },
    {
      "page": "pathwayMeasures",
      "title": "Pathway structural and functional aspects",
      "topics": [
        "pathwayMeasures"
      ]
    },
    {
      "page": "scoreSubpathways",
      "title": "Evaluate subpathways using an interacting scorng scheme (IS) for each time point.",
      "topics": [
        "scoreSubpathways"
      ]
    },
    {
      "page": "subpathwayKEGGmap",
      "title": "Create links to KEGG pathway map with highlighted subpathways.",
      "topics": [
        "subpathwayKEGGmap"
      ]
    },
    {
      "page": "subpathwayMiRNAs",
      "title": "Create a circulat plot of a subpathway and the miRNAs that target it.",
      "topics": [
        "subpathwayMiRNAs"
      ]
    },
    {
      "page": "visualizeResults",
      "title": "Visualize results in tabular form (txt, xlsx)",
      "topics": [
        "visualizeResults"
      ]
    }
  ],
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "circlize",
    "cli",
    "codetools",
    "colorspace",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "doParallel",
    "dplyr",
    "fastmap",
    "filelock",
    "foreach",
    "generics",
    "GlobalOptions",
    "glue",
    "graph",
    "hms",
    "httr",
    "httr2",
    "igraph",
    "IRanges",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "openssl",
    "openxlsx",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RBGL",
    "Rcpp",
    "RCurl",
    "rJava",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "shape",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XML",
    "xml2",
    "XVector",
    "zip"
  ],
  "_sysdeps": [
    {
      "shlib": "libjvm",
      "package": "openjdk-21-jre-headless",
      "headers": "openjdk-21-jre-headless",
      "source": "openjdk",
      "version": "21.0.11+10-1~24.04.2",
      "name": "openjdk",
      "homepage": "https://openjdk.java.net/",
      "description": "OpenJDK Java runtime, using Hotspot JIT (headless)"
    }
  ],
  "_vignettes": [
    {
      "source": "CHRONOS.Rmd",
      "filename": "CHRONOS.html",
      "title": "CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis",
      "author": "Aristidis G. Vrahatis, Konstantina Dimitrakopoulou, Panos Balomenos",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Table of Contents",
        "Package Setup",
        "User Input",
        "Default Run",
        "Citation"
      ],
      "created": "2016-04-18 21:59:28",
      "modified": "2017-04-05 00:56:23",
      "commits": 4
    }
  ],
  "_score": 3.892094602690481,
  "_indexed": false,
  "_nocasepkg": "chronos",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/CHRONOS",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.40.0",
      "date": "2026-05-31T06:34:10.000Z",
      "distro": "noble",
      "commit": "ae77439d0da121b5bceff02322475497b55ace4c",
      "fileid": "a69b780d6a2ad4ad41a3639b2c4ecf4c2598d7d5c6001ad4d12099e46edb5f86",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705336171"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.40.0",
      "date": "2026-05-31T06:34:02.000Z",
      "distro": "noble",
      "commit": "ae77439d0da121b5bceff02322475497b55ace4c",
      "fileid": "2ccc1f3f8361bca037a5fb4b0de4c555b40a91a3020a1aee074ffd237d4bdc5d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705336171"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.40.0",
      "date": "2026-05-31T06:55:22.000Z",
      "commit": "ae77439d0da121b5bceff02322475497b55ace4c",
      "fileid": "4781a91b17335758437fc83496838c85c25ad5f2786fe5b0e219420bb43ac925",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705336171"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.40.0",
      "date": "2026-05-31T06:54:56.000Z",
      "commit": "ae77439d0da121b5bceff02322475497b55ace4c",
      "fileid": "1c75e6e2d77b0fb18b82a79c5174402c5c27daeb3fe3215a66519fbb92fa2a16",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705336171"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.40.0",
      "date": "2026-05-31T06:33:14.000Z",
      "commit": "ae77439d0da121b5bceff02322475497b55ace4c",
      "fileid": "8382d3f93b270679497467cd9d6d849e52ea0dbe4b8edc39b4544702f3ade4d7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705336171"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.40.0",
      "date": "2026-05-31T06:37:16.000Z",
      "commit": "ae77439d0da121b5bceff02322475497b55ace4c",
      "fileid": "7495d4dded02a4ffa888f0da86eb0615e99c91339f8e06bcae95dca7074336f4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705336171"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.40.0",
      "date": "2026-05-31T06:38:28.000Z",
      "commit": "ae77439d0da121b5bceff02322475497b55ace4c",
      "fileid": "7dd35fb6015adc1feba0a141011afd34b057814b15f5ab707b26a80607ae2286",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705336171"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.40.0",
      "date": "2026-05-31T06:32:41.000Z",
      "commit": "ae77439d0da121b5bceff02322475497b55ace4c",
      "fileid": "f8db9c4c2340ecf2f030de02c04c7ccfa07e9a960221ed7d86b79db850e28f95",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705336171"
    }
  ]
}