{
  "_id": "6a4ca26707c3fd5c3260eb56",
  "Package": "cbaf",
  "biocViews": "Software, AssayDomain, DNAMethylation, GeneExpression,\nTranscription, Microarray,ResearchField, BiomedicalInformatics,\nComparativeGenomics, Epigenetics, Genetics, Transcriptomics",
  "Title": "Automated functions for comparing various omic data from\ncbioportal.org",
  "Version": "1.35.0",
  "Authors@R": "c(person(\"Arman\", \"Shahrisa\", role = c(\"aut\", \"cre\", \"cph\"),\nemail = \"shahrisa.arman@hotmail.com\"),\nperson(\"Maryam\", \"Tahmasebi Birgani\", role = \"aut\",\nemail = \"tahmasebi-ma@ajums.ac.ir\"))",
  "Description": "This package contains functions that allow analysing and\ncomparing omic data across various cancers/cancer subgroups\neasily. So far, it is compatible with RNA-seq, microRNA-seq,\nmicroarray and methylation datasets that are stored on\ncbioportal.org.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "NeedsCompilation": "no",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Collate": "'cbaf-obtainMultipleStudies.R' 'cbaf-obtainOneStudy.R'\n'cbaf-automatedStatistics.R' 'cbaf-availableData.R'\n'cbaf-cleanDatabase.R' 'cbaf-constants.R'\n'cbaf-heatmapOutput.R' 'cbaf-processMultipleStudies.R'\n'cbaf-processOneStudy.R' 'cbaf-xlsxOutput.R' 'zzz.R'",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libsecret-1-dev libuv1-dev libxml2-dev libssl-dev\nlibx11-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:31 UTC",
  "RemoteUrl": "https://github.com/bioc/cbaf",
  "RemoteRef": "HEAD",
  "RemoteSha": "cb59d464b42595140f50947ff9f7040d81b9b084",
  "Packaged": {
    "Date": "2026-07-07 06:43:56 UTC",
    "User": "root"
  },
  "Author": "Arman Shahrisa [aut, cre, cph],\nMaryam Tahmasebi Birgani [aut]",
  "Maintainer": "Arman Shahrisa <shahrisa.arman@hotmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "cbaf_1.35.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/2ed4fbcb37e25bbea5265cb97cd46be293dae19a2c7bf122b39b68df88c59836",
  "_filesize": 723984,
  "_sha256": "2ed4fbcb37e25bbea5265cb97cd46be293dae19a2c7bf122b39b68df88c59836",
  "_expires": "2026-10-15T06:53:25.000Z",
  "_created": "2026-07-07T06:43:56.000Z",
  "_published": "2026-07-07T06:53:27.819Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 15
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28846789453",
  "_status": "success",
  "_upstream": "https://github.com/bioc/cbaf",
  "_commit": {
    "id": "cb59d464b42595140f50947ff9f7040d81b9b084",
    "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": 1777380391
  },
  "_maintainer": {
    "name": "Arman Shahrisa",
    "email": "shahrisa.arman@hotmail.com",
    "login": "armanshahrisa",
    "description": "I'm an experimental geneticist with interests towards programming.",
    "uuid": 11501615
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85553365359,
      "time": 259,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8130069860"
    },
    {
      "job": 85553365445,
      "time": 451,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8130127688"
    },
    {
      "job": 85553365374,
      "time": 492,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8130140143"
    },
    {
      "job": 85553365360,
      "time": 270,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8130072491"
    },
    {
      "job": 85553365412,
      "time": 225,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8130059492"
    },
    {
      "job": 85552538324,
      "time": 340,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8129992256"
    },
    {
      "job": 85553365375,
      "time": 242,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8130064351"
    },
    {
      "job": 85553365424,
      "time": 351,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8130097695"
    },
    {
      "job": 85553365401,
      "time": 331,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8130091166"
    },
    {
      "job": 85553365399,
      "time": 344,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8130096107"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "BiocFileCache",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "cBioPortalData",
      "role": "Imports"
    },
    {
      "package": "genefilter",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "openxlsx",
      "role": "Imports"
    },
    {
      "package": "zip",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-43",
      "n": 3
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.35.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.34.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "assaydomain",
    "dnamethylation",
    "geneexpression",
    "transcription",
    "microarray",
    "researchfield",
    "biomedicalinformatics",
    "comparativegenomics",
    "epigenetics",
    "genetics",
    "transcriptomics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 368,
    "source": "https://www.bioconductor.org/packages/stats/bioc/cbaf"
  },
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/cbaf.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": [
    "automatedStatistics",
    "availableData",
    "cleanDatabase",
    "heatmapOutput",
    "obtainMultipleStudies",
    "obtainOneStudy",
    "processMultipleStudies",
    "processOneStudy",
    "xlsxOutput"
  ],
  "_help": [
    {
      "page": "automatedStatistics",
      "title": "Perform the requested statistics for various studies / subgroups of a study.",
      "topics": [
        "automatedStatistics"
      ]
    },
    {
      "page": "availableData",
      "title": "Check which Data types are available for each cancer study.",
      "topics": [
        "availableData"
      ]
    },
    {
      "page": "cleanDatabase",
      "title": "Clean the created database(s)",
      "topics": [
        "cleanDatabase"
      ]
    },
    {
      "page": "heatmapOutput",
      "title": "Generate heatmaps for various studies/subgroups of a study.",
      "topics": [
        "heatmapOutput"
      ]
    },
    {
      "page": "obtainMultipleStudies",
      "title": "Obtain the requested data for various cancer studies.",
      "topics": [
        "obtainMultipleStudies"
      ]
    },
    {
      "page": "obtainOneStudy",
      "title": "Obtain the requested data for various subgroups of a cancer study.",
      "topics": [
        "obtainOneStudy"
      ]
    },
    {
      "page": "processMultipleStudies",
      "title": "Check Expression/methylation Profile for various cancer studies.",
      "topics": [
        "processMultipleStudies"
      ]
    },
    {
      "page": "processOneStudy",
      "title": "Check Expression/methylation Profile for various subgroups of a cancer study.",
      "topics": [
        "processOneStudy"
      ]
    },
    {
      "page": "xlsxOutput",
      "title": "Generate excel output for various studies/subgroups of a study.",
      "topics": [
        "xlsxOutput"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "AnVIL",
    "AnVILBase",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bslib",
    "cachem",
    "caTools",
    "cBioPortalData",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "commonmark",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "dplyr",
    "DT",
    "evaluate",
    "fastmap",
    "filelock",
    "fontawesome",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "GCPtools",
    "genefilter",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicDataCommons",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "gplots",
    "gtools",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "IRanges",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "keyring",
    "knitr",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "miniUI",
    "MultiAssayExperiment",
    "openssl",
    "openxlsx",
    "otel",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "promises",
    "purrr",
    "R6",
    "RaggedExperiment",
    "rapiclient",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "readr",
    "restfulr",
    "Rhtslib",
    "rjson",
    "RJSONIO",
    "rlang",
    "rmarkdown",
    "Rsamtools",
    "RSQLite",
    "RTCGAToolbox",
    "rtracklayer",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "sass",
    "selectr",
    "Seqinfo",
    "shiny",
    "snow",
    "sourcetools",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "TCGAutils",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "tzdb",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml",
    "zip"
  ],
  "_vignettes": [
    {
      "source": "cbaf.Rmd",
      "filename": "cbaf.html",
      "title": "cbaf: an automated, easy-to-use R package for comparing omic data across multiple cancers / a cancer's subgroups",
      "author": "Arman Shahrisa",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Package Installation",
        "How to Use the cbaf",
        "main Functions",
        "availableData()",
        "cleanDatabase()",
        "processOneStudy()",
        "processMultipleStudies()",
        "Five dependant Functions",
        "obtainOneStudy()",
        "obtainMultipleStudies()",
        "automatedStatistics()",
        "heatmapOutput()",
        "xlsxOutput()"
      ],
      "created": "2017-08-16 22:30:34",
      "modified": "2024-06-02 19:33:39",
      "commits": 23
    }
  ],
  "_score": 3.4771212547196626,
  "_indexed": true,
  "_nocasepkg": "cbaf",
  "_universes": [
    "bioc",
    "armanshahrisa"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-07-07T06:48:20.000Z",
      "distro": "resolute",
      "commit": "cb59d464b42595140f50947ff9f7040d81b9b084",
      "fileid": "https://r2.ropensci.org/0243ce386a629537c770a3020d9aa562b8773e907dbf850011270fd4a74c91fd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28846789453"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-07-07T06:48:37.000Z",
      "distro": "resolute",
      "commit": "cb59d464b42595140f50947ff9f7040d81b9b084",
      "fileid": "https://r2.ropensci.org/c3e0807e285f595150f611c16459c105c9a5bd60eaa0fe11e88468aa2ee91b48",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28846789453"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-07-07T06:46:30.000Z",
      "commit": "cb59d464b42595140f50947ff9f7040d81b9b084",
      "fileid": "https://r2.ropensci.org/34e6202a204c67b874c881e77fbfed40861808c5412a273bd11c2b04133009d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28846789453"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-07-07T06:46:08.000Z",
      "commit": "cb59d464b42595140f50947ff9f7040d81b9b084",
      "fileid": "https://r2.ropensci.org/e7b38e34d05fef7f75161933cc1d98c6e5af4d53a0340c051972778ab8cccba0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28846789453"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.35.0",
      "date": "2026-07-07T06:48:44.000Z",
      "commit": "cb59d464b42595140f50947ff9f7040d81b9b084",
      "fileid": "https://r2.ropensci.org/eb106e901556dca9ce05b538982a28cf60d6e9cee3c9683bf43896ad5ac3e9c6",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28846789453"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-07-07T06:46:22.000Z",
      "commit": "cb59d464b42595140f50947ff9f7040d81b9b084",
      "fileid": "https://r2.ropensci.org/4925f6e99933fe2b59a8559c0496241fc0641099750976bddbf31edae39c58f0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28846789453"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-07-07T06:46:13.000Z",
      "commit": "cb59d464b42595140f50947ff9f7040d81b9b084",
      "fileid": "https://r2.ropensci.org/9f83ec0121382fffa6e06f9173e470fd66ce57cf1ed15fd3893f45e35335afd6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28846789453"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-07-07T06:46:35.000Z",
      "commit": "cb59d464b42595140f50947ff9f7040d81b9b084",
      "fileid": "https://r2.ropensci.org/2d75b0879f54d43d663d2a3769f3718076b3f9fbf3af92bbb49481369ebe0924",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28846789453"
    }
  ]
}