{
  "_id": "6ad607e4c5cddeca72012f3c",
  "Package": "CTexploreR",
  "Title": "Explores Cancer Testis Genes",
  "Version": "1.8.0",
  "Authors@R": "c(person(given = \"Axelle\",\nfamily = \"Loriot\",\nrole = c(\"aut\", \"cre\"),\nemail = \"axelle.loriot@uclouvain.be\",\ncomment = c(ORCID = \"0000-0002-5288-8561\")),\nperson(given = \"Julie\",\nfamily = \"Devis\",\nrole = \"aut\",\nemail = \"julie.devis@uclouvain.be\",\ncomment = c(ORCID = \"0000-0001-5525-5666\")),\nperson(given = \"Anna\",\nfamily = \"Diacofotaki\",\nrole = \"ctb\",\nemail = \"anna.diacofotaki@uclouvain.be\"),\nperson(given = \"Charles\",\nfamily = \"De Smet\",\nrole = \"ths\",\nemail = \"charles.desmet@uclouvain.be\"),\nperson(given = \"Laurent\",\nfamily = \"Gatto\",\nrole = c(\"aut\",\"ths\"),\nemail = \"laurent.gatto@uclouvain.be\",\ncomment = c(ORCID = \"0000-0002-1520-2268\")))",
  "Description": "The CTexploreR package re-defines the list of Cancer\nTestis/Germline (CT) genes. It is based on publicly available\nRNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes'\nmain characteristics. Several visualisation functions allow to\nexplore their expression in different types of tissues and\ncancer cells, or to inspect the methylation status of their\npromoters in normal tissues.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "biocViews": "Transcriptomics, Epigenetics, DifferentialExpression,\nGeneExpression, DNAMethylation, ExperimentHubSoftware,\nDataImport",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/UCLouvain-CBIO/CTexploreR",
  "BugReports": "https://github.com/UCLouvain-CBIO/CTexploreR/issues",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev perl zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 13:02:00 UTC",
  "RemoteUrl": "https://github.com/bioc/CTexploreR",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "17f6c3d4485df49a9a51fbebbfd0cbb9e3a7a01c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-19 11:53:07 UTC",
    "User": "root"
  },
  "Author": "Axelle Loriot [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-5288-8561>),\nJulie Devis [aut] (ORCID: <https://orcid.org/0000-0001-5525-5666>),\nAnna Diacofotaki [ctb],\nCharles De Smet [ths],\nLaurent Gatto [aut, ths] (ORCID:\n<https://orcid.org/0000-0002-1520-2268>)",
  "Maintainer": "Axelle Loriot <axelle.loriot@uclouvain.be>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "CTexploreR_1.8.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/a3f7b60a80392a5d54bc501d03e148d099731acf758655ae74bf1acf91c33f93",
  "_filesize": 7117684,
  "_sha256": "a3f7b60a80392a5d54bc501d03e148d099731acf758655ae74bf1acf91c33f93",
  "_expires": "2027-01-27T12:06:57.000Z",
  "_created": "2026-10-19T11:53:07.000Z",
  "_published": "2026-10-19T12:07:00.186Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39246522889",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 9
  },
  "_upstream": "https://github.com/bioc/CTexploreR",
  "_commit": {
    "id": "17f6c3d4485df49a9a51fbebbfd0cbb9e3a7a01c",
    "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": 1777381320
  },
  "_maintainer": {
    "name": "Axelle Loriot",
    "email": "axelle.loriot@uclouvain.be",
    "login": "aloriot",
    "description": "",
    "uuid": 43926178,
    "orcid": "0000-0002-5288-8561"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 118044450625,
      "time": 186,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12184127975"
    },
    {
      "job": 118044450641,
      "time": 725,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12184836626"
    },
    {
      "job": 118044450523,
      "time": 533,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12184064053"
    },
    {
      "job": 118044450744,
      "time": 535,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12184069073"
    },
    {
      "job": 118044450996,
      "time": 695,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12184752317"
    },
    {
      "job": 118039789604,
      "time": 695,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12182774951"
    },
    {
      "job": 118044450614,
      "time": 145,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12183948244"
    },
    {
      "job": 118044450672,
      "time": 528,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12184492566"
    },
    {
      "job": 118044450693,
      "time": 445,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12185275153"
    },
    {
      "job": 118044450551,
      "time": 545,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12183904226"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3",
      "role": "Depends"
    },
    {
      "package": "CTdata",
      "version": ">= 1.5.3",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "MatrixGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "InteractiveComplexHeatmap",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "transcriptomics",
    "epigenetics",
    "differentialexpression",
    "geneexpression",
    "dnamethylation",
    "experimenthubsoftware",
    "dataimport",
    "bioconductor"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "juliedevis",
      "count": 140,
      "uuid": 78104704
    },
    {
      "user": "aloriot",
      "count": 133,
      "uuid": 43926178
    },
    {
      "user": "lgatto",
      "count": 36,
      "uuid": 384198
    },
    {
      "user": "jwokaty",
      "count": 6,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 478,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 386,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CTexploreR"
  },
  "_devurl": "https://github.com/uclouvain-cbio/ctexplorer",
  "_searchresults": 10,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/CTexploreR.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/uclouvain-cbio/ctexplorer",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "all_genes",
    "CCLE_expression",
    "CT_correlated_genes",
    "CT_genes",
    "DAC_induction",
    "embryo_expression",
    "embryos_mean_methylation",
    "fetal_germcells_expression",
    "fetal_germcells_mean_methylation",
    "GTEX_expression",
    "hESC_expression",
    "hESC_mean_methylation",
    "HPA_cell_type_expression",
    "normal_tissue_expression_multimapping",
    "normal_tissues_mean_methylation",
    "normal_tissues_methylation",
    "oocytes_expression",
    "TCGA_expression",
    "TCGA_methylation_expression_correlation",
    "testis_expression"
  ],
  "_help": [
    {
      "page": "all_genes",
      "title": "All genes description table",
      "topics": [
        "all_genes"
      ]
    },
    {
      "page": "CCLE_expression",
      "title": "Gene expression in CCLE Tumors",
      "topics": [
        "CCLE_expression"
      ]
    },
    {
      "page": "CT_correlated_genes",
      "title": "Gene correlations in CCLE cancer cell lines",
      "topics": [
        "CT_correlated_genes"
      ]
    },
    {
      "page": "CT_genes",
      "title": "CT genes description table",
      "topics": [
        "CT_genes"
      ]
    },
    {
      "page": "DAC_induction",
      "title": "Gene expression in cells treated or not by a demethylating agent",
      "topics": [
        "DAC_induction"
      ]
    },
    {
      "page": "embryo_expression",
      "title": "Gene expression in human embryos",
      "topics": [
        "embryo_expression"
      ]
    },
    {
      "page": "embryos_mean_methylation",
      "title": "Promoter methylation of any gene in early embryos",
      "topics": [
        "embryos_mean_methylation"
      ]
    },
    {
      "page": "fetal_germcells_expression",
      "title": "Gene expression in fetal germ cells",
      "topics": [
        "fetal_germcells_expression"
      ]
    },
    {
      "page": "fetal_germcells_mean_methylation",
      "title": "Promoter methylation of any gene in fetal germ cells",
      "topics": [
        "fetal_germcells_mean_methylation"
      ]
    },
    {
      "page": "GTEX_expression",
      "title": "Gene expression in normal tissues (GTEx)",
      "topics": [
        "GTEX_expression"
      ]
    },
    {
      "page": "hESC_expression",
      "title": "Gene expression in human embryonic stem cells",
      "topics": [
        "hESC_expression"
      ]
    },
    {
      "page": "hESC_mean_methylation",
      "title": "Promoter methylation of any gene in hESC",
      "topics": [
        "hESC_mean_methylation"
      ]
    },
    {
      "page": "HPA_cell_type_expression",
      "title": "Gene expression in different human cell types",
      "topics": [
        "HPA_cell_type_expression"
      ]
    },
    {
      "page": "normal_tissue_expression_multimapping",
      "title": "Expression values (TPM) of genes in normal tissues with or without multimapping",
      "topics": [
        "normal_tissue_expression_multimapping"
      ]
    },
    {
      "page": "normal_tissues_mean_methylation",
      "title": "Promoter methylation of any gene in normal tissues",
      "topics": [
        "normal_tissues_mean_methylation"
      ]
    },
    {
      "page": "normal_tissues_methylation",
      "title": "Methylation of CpGs located in promoters in normal tissues",
      "topics": [
        "normal_tissues_methylation"
      ]
    },
    {
      "page": "oocytes_expression",
      "title": "Gene expression in oocytes",
      "topics": [
        "oocytes_expression"
      ]
    },
    {
      "page": "set_fontsize",
      "title": "Determine font size",
      "topics": [
        "set_fontsize"
      ]
    },
    {
      "page": "TCGA_expression",
      "title": "Gene expression in TCGA tumors",
      "topics": [
        "TCGA_expression"
      ]
    },
    {
      "page": "TCGA_methylation_expression_correlation",
      "title": "Methylation-Expression correlation of any genes in TCGA samples",
      "topics": [
        "TCGA_methylation_expression_correlation"
      ]
    },
    {
      "page": "testis_expression",
      "title": "Gene expression in testis cells",
      "topics": [
        "testis_expression"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CTexploreR/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationHub",
    "askpass",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocManager",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "ComplexHeatmap",
    "cpp11",
    "crayon",
    "CTdata",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "doParallel",
    "dplyr",
    "ExperimentHub",
    "farver",
    "fastmap",
    "filelock",
    "foreach",
    "generics",
    "GenomicRanges",
    "GetoptLong",
    "ggplot2",
    "ggrepel",
    "GlobalOptions",
    "glue",
    "gtable",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "rjson",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "shape",
    "SingleCellExperiment",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "CTexploreR.Rmd",
      "filename": "CTexploreR.html",
      "title": "Cancer Testis explorer",
      "author": "Julie Devis, Laurent Gatto, Axelle Loriot",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "CT genes",
        "CT gene selection",
        "Testis-specific expression",
        "Activation in cancer cell lines and TCGA tumors",
        "IGV visualisation",
        "Regulation by methylation",
        "Available functions",
        "Expression in normal healthy adult tissues",
        "GTEX_expression()",
        "normal_tissue_expression_multimapping()",
        "testis_expression()",
        "oocytes_expression()",
        "HPA_cell_type_expression()",
        "Expression in fetal cells",
        "embryo_expression()",
        "fetal_germcells_expression()",
        "hESC_expression()",
        "Expression in cancer cells and samples",
        "CCLE_expression()",
        "CT_correlated_genes()",
        "TCGA_expression()",
        "Methylation analysis",
        "DAC_induction()",
        "normal_tissues_methylation()",
        "normal_tissues_mean_methylation()",
        "embryos_mean_methylation()",
        "fetal_germcells_mean_methylation()",
        "hESC_mean_methylation()",
        "TCGA_methylation_expression_correlation()",
        "Interactive heatmaps",
        "Bibliography",
        "Session information"
      ],
      "created": "2023-02-24 17:17:41",
      "modified": "2024-10-28 10:23:55",
      "commits": 23
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": false,
  "_nocasepkg": "ctexplorer",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/CTexploreR",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.8.0",
      "date": "2026-10-19T11:58:27.000Z",
      "distro": "resolute",
      "commit": "17f6c3d4485df49a9a51fbebbfd0cbb9e3a7a01c",
      "fileid": "https://r2.ropensci.org/3e4c1395ea42cae0d852477cdcfe5e7e7d5f5c9caa21b2d5612a8daf415be883",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39246522889"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.8.0",
      "date": "2026-10-19T11:56:49.000Z",
      "distro": "resolute",
      "commit": "17f6c3d4485df49a9a51fbebbfd0cbb9e3a7a01c",
      "fileid": "https://r2.ropensci.org/e94b8a0d320d22b621ac8d0dc7b7ee29ff4582c2b6cd77cfd94768b507ac67eb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39246522889"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.8.0",
      "date": "2026-10-19T11:55:51.000Z",
      "commit": "17f6c3d4485df49a9a51fbebbfd0cbb9e3a7a01c",
      "fileid": "https://r2.ropensci.org/021641a3f8c4edc32eac1bad9d4008ccd9717876c943a04a289814f2faaa3cfe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39246522889"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.8.0",
      "date": "2026-10-19T11:56:44.000Z",
      "commit": "17f6c3d4485df49a9a51fbebbfd0cbb9e3a7a01c",
      "fileid": "https://r2.ropensci.org/54bd3d728cc7629aa78ab29dccee951cc9af14e2253696b617e2bf16e9fa5c12",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39246522889"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.8.0",
      "date": "2026-10-19T11:56:06.000Z",
      "commit": "17f6c3d4485df49a9a51fbebbfd0cbb9e3a7a01c",
      "fileid": "https://r2.ropensci.org/6f253e2a62806ae39f0aa05a9494e49a99e1112158275fab867f3597400b03bf",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39246522889"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-10-19T11:55:06.000Z",
      "commit": "17f6c3d4485df49a9a51fbebbfd0cbb9e3a7a01c",
      "fileid": "https://r2.ropensci.org/ffc66b4b6ec0e91e9f1e512c83468f1443315d2830d4a43fd868ee902521a56e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39246522889"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-10-19T11:54:54.000Z",
      "commit": "17f6c3d4485df49a9a51fbebbfd0cbb9e3a7a01c",
      "fileid": "https://r2.ropensci.org/534bf2b45efbb4022b6d089f95a4effb80ff1e8c46e39fd013588d003b4a12c5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39246522889"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-10-19T11:55:02.000Z",
      "commit": "17f6c3d4485df49a9a51fbebbfd0cbb9e3a7a01c",
      "fileid": "https://r2.ropensci.org/585f5fc05da8685ebe1320579a2457c23d2fdc046656c714cb19ec1814028ca0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39246522889"
    }
  ]
}