{ "_id": "6aca24aafe5cc25786e850cd", "Package": "RTCGA.methylation", "Type": "Package", "Title": "Methylation datasets from The Cancer Genome Atlas Project", "Version": "1.40.0", "Date": "2015-12-23", "Authors@R": "c( person(\"Marcin\", \"Kosinski\", role = c(\"aut\", \"cre\"), email =\n\"m.p.kosinski@gmail.com\"), person(\"Witold\", \"Chodor\", role = c(\"aut\"), email =\n\"witoldchodor@gmail.com\") )", "Description": "Package provides methylation (humanmethylation27) datasets\nfrom The Cancer Genome Atlas Project for all available cohorts\ntypes from http://gdac.broadinstitute.org/. Data format is\nexplained here\nhttps://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from\n2015-11-01 snapshot.", "License": "GPL-2", "LazyData": "TRUE", "BugReports": "https://github.com/RTCGA/RTCGA/issues", "biocViews": "AnnotationData", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "RoxygenNote": "7.1.1", "Author": "Marcin Kosinski [aut, cre], Witold Chodor [aut]", "Maintainer": "Marcin Kosinski ", "Config/pak/sysreqs": "cmake make libicu-dev libjpeg-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:29:00 UTC", "RemoteUrl": "https://github.com/bioc/RTCGA.methylation", "RemoteRef": "RELEASE_3_23", "RemoteSha": "dafcf0612572f7736989cebd165b908baa6a5d4f", "Packaged": { "Date": "2026-10-10 11:10:13 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "RTCGA.methylation_1.40.0.tar.gz", "_fileid": "https://r2.ropensci.org/e78bf82167661697468889f0cb09c1199fe1bce501feb02c264e96cedbe8f4b3", "_filesize": 704397795, "_sha256": "e78bf82167661697468889f0cb09c1199fe1bce501feb02c264e96cedbe8f4b3", "_expires": "2027-01-18T11:42:15.000Z", "_created": "2026-10-10T11:10:13.000Z", "_published": "2026-10-10T11:42:33.954Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047170978", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 2, "warning": 2, "note": 13 }, "_upstream": "https://github.com/bioc/RTCGA.methylation", "_commit": { "id": "dafcf0612572f7736989cebd165b908baa6a5d4f", "author": "lshep ", "committer": "lshep ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379340 }, "_maintainer": { "name": "Marcin Kosinski", "email": "m.p.kosinski@gmail.com", "login": "marcinkosinski", "description": "\n", "uuid": 6773454 }, "_distro": "resolute", "_jobs": [ { "job": 114202101267, "time": 157, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11667983622" }, { "job": 114202101242, "time": 822, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11668249403" }, { "job": 114202101302, "time": 981, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11668204758" }, { "job": 114198975608, "time": 1107, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11667928266" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3.0", "role": "Depends" }, { "package": "RTCGA", "role": "Depends" }, { "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": "1.39.0", "bioc": "3.24", "repository": "data/experiment" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23", "repository": "data/experiment" } ], "_topics": [ "annotationdata", "datapkg" ], "_stars": 51, "_contributors": [ { "user": "marcinkosinski", "count": 87, "uuid": 6773454 }, { "user": "pbiecek", "count": 37, "uuid": 4624318 }, { "user": "quares", "count": 6, "uuid": 7707019 }, { "user": "wchodor", "count": 4, "uuid": 15180983 }, { "user": "kassambara", "count": 2, "uuid": 3313355 }, { "user": "jimhester", "count": 2, "uuid": 205275 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 22, "_devurl": "https://github.com/rtcga/rtcga", "_searchresults": 7, "_datapkg": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/RTCGA.methylation.html" ], "_cranurl": false, "_exports": [], "_datasets": [ { "name": "BRCA.methylation", "title": "Methylation datasets from TCGA project", "object": "BRCA.methylation", "class": [ "data.frame" ], "fields": [], "rows": 343, "table": true, "tojson": true }, { "name": "COAD.methylation", "title": "Methylation datasets from TCGA project", "object": "COAD.methylation", "class": [ "data.frame" ], "fields": [], "rows": 202, "table": true, "tojson": true }, { "name": "COADREAD.methylation", "title": "Methylation datasets from TCGA project", "object": "COADREAD.methylation", "class": [ "data.frame" ], "fields": [], "rows": 275, "table": true, "tojson": true }, { "name": "GBM.methylation", "title": "Methylation datasets from TCGA project", "object": "GBM.methylation", "class": [ "data.frame" ], "fields": [], "rows": 285, "table": true, "tojson": true }, { "name": "GBMLGG.methylation", "title": "Methylation datasets from TCGA project", "object": "GBMLGG.methylation", "class": [ "data.frame" ], "fields": [], "rows": 285, "table": true, "tojson": true }, { "name": "KIPAN.methylation", "title": "Methylation datasets from TCGA project", "object": "KIPAN.methylation", "class": [ "data.frame" ], "fields": [], "rows": 439, "table": true, "tojson": true }, { "name": "KIRC.methylation", "title": "Methylation datasets from TCGA project", "object": "KIRC.methylation", "class": [ "data.frame" ], "fields": [], "rows": 418, "table": true, "tojson": true }, { "name": "KIRP.methylation", "title": "Methylation datasets from TCGA project", "object": "KIRP.methylation", "class": [ "data.frame" ], "fields": [], "rows": 21, "table": true, "tojson": true }, { "name": "LAML.methylation", "title": "Methylation datasets from TCGA project", "object": "LAML.methylation", "class": [ "data.frame" ], "fields": [], "rows": 194, "table": true, "tojson": true }, { "name": "LUAD.methylation", "title": "Methylation datasets from TCGA project", "object": "LUAD.methylation", "class": [ "data.frame" ], "fields": [], "rows": 150, "table": true, "tojson": true }, { "name": "LUSC.methylation", "title": "Methylation datasets from TCGA project", "object": "LUSC.methylation", "class": [ "data.frame" ], "fields": [], "rows": 160, "table": true, "tojson": true }, { "name": "OV.methylation1", "title": "Methylation datasets from TCGA project", "object": "OV.methylation1", "class": [ "data.frame" ], "fields": [], "rows": 300, "table": true, "tojson": true }, { "name": "OV.methylation2", "title": "Methylation datasets from TCGA project", "object": "OV.methylation2", "class": [ "data.frame" ], "fields": [], "rows": 312, "table": true, "tojson": true }, { "name": "READ.methylation", "title": "Methylation datasets from TCGA project", "object": "READ.methylation", "class": [ "data.frame" ], "fields": [], "rows": 73, "table": true, "tojson": true }, { "name": "STAD.methylation", "title": "Methylation datasets from TCGA project", "object": "STAD.methylation", "class": [ "data.frame" ], "fields": [], "rows": 73, "table": true, "tojson": true }, { "name": "STES.methylation", "title": "Methylation datasets from TCGA project", "object": "STES.methylation", "class": [ "data.frame" ], "fields": [], "rows": 73, "table": true, "tojson": true }, { "name": "UCEC.methylation", "title": "Methylation datasets from TCGA project", "object": "UCEC.methylation", "class": [ "data.frame" ], "fields": [], "rows": 118, "table": true, "tojson": true } ], "_help": [ { "page": "methylation", "title": "Methylation datasets from TCGA project", "topics": [ "BRCA.methylation", "BRCA.methylation,COAD.methylation,COADREAD.methylation,GBM.methylation,GBMLGG.methylation,KIPAN.methylation,KIRC.methylation,KIRP.methylation,LAML.methylation,LUAD.methylation,LUSC.methylation,OV.methylation,OV.methylation1,OV.methylation2,READ.methylation,STAD.methylation,STES.methylation,UCEC.methylation", "COAD.methylation", "COADREAD.methylation", "GBM.methylation", "GBMLGG.methylation", "KIPAN.methylation", "KIRC.methylation", "KIRP.methylation", "LAML.methylation", "LUAD.methylation", "LUSC.methylation", "methylation", "OV.methylation1", "OV.methylation2", "READ.methylation", "STAD.methylation", "STES.methylation", "UCEC.methylation" ] } ], "_readme": "https://github.com/bioc/RTCGA.methylation/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "askpass", "assertthat", "backports", "base64enc", "bitops", "boot", "broom", "bslib", "cachem", "car", "carData", "cli", "colorspace", "commonmark", "corrplot", "cowplot", "cpp11", "curl", "data.table", "Deriv", "digest", "doBy", "dplyr", "evaluate", "exactRankTests", "farver", "fastmap", "fontawesome", "forecast", "Formula", "fracdiff", "fs", "generics", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "ggtext", "ggthemes", "glue", "gridExtra", "gridtext", "gtable", "highr", "htmltools", "httr", "isoband", "jpeg", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "litedown", "lme4", "lmtest", "magrittr", "markdown", "MASS", "Matrix", "MatrixModels", "maxstat", "memoise", "mgcv", "mime", "minqa", "modelr", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "pbkrtest", "pillar", "pkgconfig", "png", "polynom", "purrr", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "Rdpack", "reformulas", "rlang", "rmarkdown", "rstatix", "RTCGA", "rvest", "S7", "sass", "scales", "selectr", "SparseM", "stringi", "stringr", "survival", "survminer", "sys", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "zoo" ], "_vignettes": [ { "source": "downloading_methylation_datasets.Rmd", "filename": "downloading_methylation_datasets.html", "title": "Using RTCGA package to download methylation data that are included in RTCGA.methylation package", "author": "Marcin Kosiński", "engine": "knitr::rmarkdown", "headings": [ "RTCGA package", "How to download methylation data to gain the same datasets as in RTCGA.methylation package?", "Available cohorts", "Downloading tarred files", "Reading downloaded methylation dataset", "Shortening paths and directories", "Removing NA files from data2", "Paths to methylation data", "Reading methylation data using readTCGA", "Saving methylation data to RTCGA.methylation package" ], "created": "2016-01-26 17:46:04", "modified": "2018-08-31 18:02:33", "commits": 2 } ], "_score": 7.406540180433955, "_indexed": false, "_nocasepkg": "rtcga.methylation", "_universes": [ "bioc-release" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.40.0", "date": "2026-10-10T11:27:18.000Z", "distro": "resolute", "commit": "dafcf0612572f7736989cebd165b908baa6a5d4f", "fileid": "https://r2.ropensci.org/8c144fe354d11a5d315d225e89b1ead6fd37c9017473df3d9f1c315b95e2aafc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047170978" }, { "r": "4.6.1", "os": "linux", "version": "1.40.0", "date": "2026-10-10T11:27:57.000Z", "distro": "resolute", "commit": "dafcf0612572f7736989cebd165b908baa6a5d4f", "fileid": "https://r2.ropensci.org/4d47e85845a3007c10e620b84d537752f2df53dccaa1708deedc25a7c6fe5f21", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047170978" } ] }