{ "_id": "6a12beb2acfb0bcc41d1d5e2", "Package": "TCGAretriever", "Type": "Package", "Title": "Retrieve Genomic and Clinical Data from CBioPortal Including\nTCGA Data", "Version": "1.10.3", "Date": "2026-02-23", "Authors@R": "person(\"Damiano\", \"Fantini\", , \"damiano.fantini@gmail.com\", role = c(\"aut\", \"cre\"))", "Maintainer": "Damiano Fantini ", "VignetteBuilder": "knitr", "Description": "The Cancer Genome Atlas (TCGA) is a program aimed at\nimproving our understanding of Cancer Biology. Several TCGA\nDatasets are available online. 'TCGAretriever' helps accessing\nand downloading TCGA data hosted on 'cBioPortal' via its Web\nInterface (see for more\ninformation).", "License": "GPL-3", "LazyData": "true", "URL": "https://www.data-pulse.com/dev_site/TCGAretriever/", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libicu-dev libssl-dev", "Repository": "https://dami82.r-universe.dev", "Date/Publication": "2026-02-23 05:17:13 UTC", "RemoteUrl": "https://github.com/dami82/tcgaretriever", "RemoteRef": "HEAD", "RemoteSha": "8b8ba1d61503dbfb5ceb2093751a1eb0149f7ff0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-24 08:59:40 UTC", "User": "root" }, "Author": "Damiano Fantini [aut, cre]", "MD5sum": "47f117c8eb0e3cf71598864f166a1cce", "_user": "dami82", "_type": "src", "_file": "TCGAretriever_1.10.3.tar.gz", "_fileid": "cd95f3ded8661068a488c46c22d1794d1d1125b3444d7801d6073d4c45e116c7", "_filesize": 473607, "_sha256": "cd95f3ded8661068a488c46c22d1794d1d1125b3444d7801d6073d4c45e116c7", "_created": "2026-05-24T08:59:40.000Z", "_published": "2026-05-24T09:02:42.311Z", "_distro": "noble", "_jobs": [ { "job": 77585412156, "time": 147, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7183862547" }, { "job": 77585412145, "time": 156, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7183863364" }, { "job": 77585412151, "time": 129, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7183857703" }, { "job": 77585412149, "time": 130, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7183857267" }, { "job": 77585236584, "time": 190, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7183844859" }, { "job": 77585412147, "time": 120, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7183859047" }, { "job": 77585412159, "time": 86, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7183854873" }, { "job": 77585412155, "time": 74, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7183853373" }, { "job": 77585412158, "time": 74, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7183853410" } ], "_buildurl": "https://github.com/r-universe/dami82/actions/runs/26356918601", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/dami82/tcgaretriever", "_commit": { "id": "8b8ba1d61503dbfb5ceb2093751a1eb0149f7ff0", "author": "dami82 ", "committer": "dami82 ", "message": "Include RHUB workflow\n", "time": 1771823833 }, "_maintainer": { "name": "Damiano Fantini", "email": "damiano.fantini@gmail.com", "login": "dami82", "description": "", "uuid": 14799776 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "httr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "stats", "role": "Suggests" }, { "package": "utils", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" } ], "_owner": "dami82", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-47", "n": 4 }, { "week": "2026-07", "n": 2 }, { "week": "2026-09", "n": 11 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "dami82", "count": 23, "uuid": 14799776 } ], "_userbio": { "uuid": 14799776, "type": "user", "name": "Damiano Fantini" }, "_downloads": { "count": 305, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TCGAretriever" }, "_mentions": 1, "_devurl": "https://github.com/dami82/tcgaretriever", "_searchresults": 35, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/TCGAretriever.html", "manual.pdf" ], "_homeurl": "https://github.com/dami82/tcgaretriever", "_realowner": "dami82", "_cranurl": true, "_releases": [ { "version": "1.1", "date": "2016-07-13" }, { "version": "1.3", "date": "2016-07-30" }, { "version": "1.5", "date": "2019-12-17" }, { "version": "1.7", "date": "2023-07-10" }, { "version": "1.9.1", "date": "2024-01-23" }, { "version": "1.10.1", "date": "2025-11-20" }, { "version": "1.10.3", "date": "2026-02-23" } ], "_exports": [ "check_TCGAretriever_connection", "expand_cases", "fetch_all_tcgadata", "get_cancer_studies", "get_cancer_types", "get_case_lists", "get_clinical_data", "get_gene_identifiers", "get_genetic_profiles", "get_molecular_data", "get_mutation_data", "make_groups" ], "_datasets": [ { "name": "blcaOutputExamples", "title": "TCGAretriever Examples", "object": "blcaOutputExamples", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "blcaOutputExamples", "title": "TCGAretriever Examples", "topics": [ "blcaOutputExamples" ] }, { "page": "check_TCGAretriever_connection", "title": "Check Connection to the cBioPortal Server", "topics": [ "check_TCGAretriever_connection" ] }, { "page": "expand_cases", "title": "Samples Included in a List of Samples.", "topics": [ "expand_cases" ] }, { "page": "fetch_all_tcgadata", "title": "Fetch All Molecular Data for a Cancer Profile of Interest.", "topics": [ "fetch_all_tcgadata" ] }, { "page": "get_cancer_studies", "title": "Retrieve the List of Cancer Studies Available at cbioportal.", "topics": [ "get_cancer_studies" ] }, { "page": "get_cancer_types", "title": "Retrieve Cancer Types.", "topics": [ "get_cancer_types" ] }, { "page": "get_case_lists", "title": "Retrieve Case List Available for a Specific Cancer Study.", "topics": [ "get_case_lists" ] }, { "page": "get_clinical_data", "title": "Retrieve Clinical Information for a Cancer Study.", "topics": [ "get_clinical_data" ] }, { "page": "get_gene_identifiers", "title": "Retrieve All Gene Identifiers", "topics": [ "get_gene_identifiers" ] }, { "page": "get_genetic_profiles", "title": "Retrieve Genetic Profiles for a TCGA Study of Interest", "topics": [ "get_genetic_profiles" ] }, { "page": "get_molecular_data", "title": "Retrieve Molecular Data corresponding to a Genetic Profile of Interest.", "topics": [ "get_molecular_data" ] }, { "page": "get_mutation_data", "title": "Retrieve Mutation Data corresponding to a Genetic Profile of Interest.", "topics": [ "get_mutation_data" ] }, { "page": "make_groups", "title": "Split Numeric Vectors in Groups.", "topics": [ "make_groups" ] } ], "_readme": "https://github.com/dami82/tcgaretriever/raw/HEAD/README.md", "_rundeps": [ "askpass", "cli", "curl", "glue", "httr", "jsonlite", "lifecycle", "magrittr", "mime", "openssl", "plyr", "R6", "Rcpp", "reshape2", "rlang", "stringi", "stringr", "sys", "vctrs" ], "_vignettes": [ { "source": "get_started_with_TCGAretriever.Rmd", "filename": "get_started_with_TCGAretriever.html", "title": "Get started with TCGAretriever", "author": "Damiano Fantini", "engine": "knitr::rmarkdown", "headings": [ "Basic Operations", "Connection to the cBioPortal Server", "Cancer Study IDs", "Genetic Profiles (Assays) and Case Lists", "Retrieve Genomic Data", "Retrieve Data for all available genes", "Examples and visualizations", "Relationship between E2F1 and EZH2 in BRCA", "E2F1 Expression vs. Binned EZH2 Expression in BRCA", "Relationship between HMGA1 and TP53 with respect to TP53 mutation status in BRCA", "SessionInfo" ], "created": "2026-02-23 04:47:34", "modified": "2026-02-23 05:16:41", "commits": 5 } ], "_score": 4.720159303405957, "_indexed": true, "_nocasepkg": "tcgaretriever", "_universes": [ "dami82" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.10.3", "date": "2026-05-24T09:02:06.000Z", "distro": "noble", "commit": "8b8ba1d61503dbfb5ceb2093751a1eb0149f7ff0", "fileid": "485003a530ddbb6da41188490b6bdd81e870ba8c6731a57dcae4708a592f5f34", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dami82/actions/runs/26356918601" }, { "r": "4.6.0", "os": "linux", "version": "1.10.3", "date": "2026-05-24T09:02:14.000Z", "distro": "noble", "commit": "8b8ba1d61503dbfb5ceb2093751a1eb0149f7ff0", "fileid": "434f4a636d8fc7e200669d194ca215b61dd79da2ede1b67fa3381ae7393b0fb1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dami82/actions/runs/26356918601" }, { "r": "4.5.3", "os": "mac", "version": "1.10.3", "date": "2026-05-24T09:01:33.000Z", "commit": "8b8ba1d61503dbfb5ceb2093751a1eb0149f7ff0", "fileid": "ef2418de555606ce7958ea20d0618bacbb34e1db31594c3b018ba41469c8618d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dami82/actions/runs/26356918601" }, { "r": "4.6.0", "os": "mac", "version": "1.10.3", "date": "2026-05-24T09:01:26.000Z", "commit": "8b8ba1d61503dbfb5ceb2093751a1eb0149f7ff0", "fileid": "3682e1ecd08615ec2ec7593d33479f590a95831603a8bf2e8d9dc42ea13eec98", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dami82/actions/runs/26356918601" }, { "r": "4.6.0", "os": "wasm", "version": "1.10.3", "date": "2026-05-24T09:01:54.000Z", "commit": "8b8ba1d61503dbfb5ceb2093751a1eb0149f7ff0", "fileid": "6cac52a7f30e74fe90c54db4fa7317d8c4ecb91933a0b07c30a99fc781956f0a", "status": "success", "buildurl": "https://github.com/r-universe/dami82/actions/runs/26356918601" }, { "r": "4.7.0", "os": "win", "version": "1.10.3", "date": "2026-05-24T09:00:59.000Z", "commit": "8b8ba1d61503dbfb5ceb2093751a1eb0149f7ff0", "fileid": "0a14bb1abf7ed0cab5278d59e5896dcd5a84cfcb10ed68a8250f143d11efd61a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dami82/actions/runs/26356918601" }, { "r": "4.5.3", "os": "win", "version": "1.10.3", "date": "2026-05-24T09:00:46.000Z", "commit": "8b8ba1d61503dbfb5ceb2093751a1eb0149f7ff0", "fileid": "3de415d1d478d29f6e521354b83b8ff5fa85a33413e7ce70228f22d789791ea0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dami82/actions/runs/26356918601" }, { "r": "4.6.0", "os": "win", "version": "1.10.3", "date": "2026-05-24T09:00:48.000Z", "commit": "8b8ba1d61503dbfb5ceb2093751a1eb0149f7ff0", "fileid": "b3098a6f2ccd9837d090897c3066325f551e5edb8434006c272acda1e3605817", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dami82/actions/runs/26356918601" } ] }