{ "_id": "6a1ae77c1d7bb097a09f143b", "Package": "cbpManager", "Type": "Package", "Title": "Generate, manage, and edit data and metadata files suitable for\nthe import in cBioPortal for Cancer Genomics", "Version": "1.21.0", "Date": "2021-03-16", "Authors@R": "c(\nperson(given = \"Arsenij\", family = \"Ustjanzew\", email = \"arsenij.ustjanzew@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0002-1014-4521\")),\nperson(\"Federico\", \"Marini\", role = \"aut\", email = \"marinif@uni-mainz.de\", comment = c(ORCID = '0000-0003-3252-7758')))", "Description": "This R package provides an R Shiny application that\nenables the user to generate, manage, and edit data and\nmetadata files suitable for the import in cBioPortal for Cancer\nGenomics. Create cancer studies and edit its metadata. Upload\nmutation data of a patient that will be concatenated to the\ndata_mutation_extended.txt file of the study. Create and edit\nclinical patient data, sample data, and timeline data. Create\ncustom timeline tracks for patients.", "License": "AGPL-3 + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "URL": "https://arsenij-ust.github.io/cbpManager/index.html", "BugReports": "https://github.com/arsenij-ust/cbpManager/issues", "StagedInstall": "no", "Collate": "'basilisk.R' 'dynamicTable.R' 'modulesResourceButtons.R'\n'cbpManager-pkg.R' 'functions.R' 'global.R' 'cbpManager.R'\n'shinyAppServer.R' 'shinyAppUI.R'", "biocViews": "ImmunoOncology, DataImport, DataRepresentation, GUI,\nThirdPartyClient, Preprocessing, Visualization", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev python3\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:01 UTC", "RemoteUrl": "https://github.com/bioc/cbpManager", "RemoteRef": "HEAD", "RemoteSha": "f2bfaa697f1902924f2dee4dbde49fdfe236a80c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:37:20 UTC", "User": "root" }, "Author": "Arsenij Ustjanzew [aut, cre, cph] (ORCID:\n),\nFederico Marini [aut] (ORCID: )", "Maintainer": "Arsenij Ustjanzew ", "MD5sum": "c5fddf9242af8ccdd555a19bc4dcda5b", "_user": "bioc", "_type": "src", "_file": "cbpManager_1.21.0.tar.gz", "_fileid": "17906cc2687e6c07e95d274ddf55c675ee1166c66b96889cfb20114de08c842b", "_filesize": 2543651, "_sha256": "17906cc2687e6c07e95d274ddf55c675ee1166c66b96889cfb20114de08c842b", "_created": "2026-05-30T09:37:20.000Z", "_published": "2026-05-30T13:34:51.974Z", "_jobs": [ { "job": 78640114033, "time": 164, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307333393" }, { "job": 78640114040, "time": 162, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307333196" }, { "job": 78640114036, "time": 194, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307336183" }, { "job": 78640114041, "time": 134, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308549822" }, { "job": 78640114045, "time": 109, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308544931" }, { "job": 78639516023, "time": 215, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307230447" }, { "job": 78640114024, "time": 137, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307330722" }, { "job": 78640114057, "time": 123, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307330304" }, { "job": 78640114047, "time": 112, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307329210" }, { "job": 78640114043, "time": 165, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307334394" } ], "_bioccheck": { "error": 1, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676150350", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/cbpManager", "_commit": { "id": "f2bfaa697f1902924f2dee4dbde49fdfe236a80c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380961 }, "_maintainer": { "name": "Arsenij Ustjanzew", "email": "arsenij.ustjanzew@gmail.com", "login": "arsenij-ust", "description": "", "uuid": 61419866, "orcid": "0000-0002-1014-4521" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "shiny", "role": "Depends" }, { "package": "shinydashboard", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "htmltools", "role": "Imports" }, { "package": "vroom", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "rapportools", "role": "Imports" }, { "package": "basilisk", "role": "Imports" }, { "package": "reticulate", "role": "Imports" }, { "package": "shinyBS", "role": "Imports" }, { "package": "shinycssloaders", "role": "Imports" }, { "package": "rintrojs", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "markdown", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "dataimport", "datarepresentation", "gui", "thirdpartyclient", "preprocessing", "visualization", "cancer-genomics", "cbioportal", "clinical-data", "filegenerator", "mutation-data", "patient-data" ], "_stars": 8, "_contributors": [ { "user": "arsenij-ust", "count": 104, "uuid": 61419866 }, { "user": "federicomarini", "count": 22, "uuid": 7447478 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "nturaga", "count": 6, "uuid": 2746443 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 382, "source": "https://www.bioconductor.org/packages/stats/bioc/cbpManager" }, "_devurl": "https://github.com/arsenij-ust/cbpmanager", "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/cbpManager.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/arsenij-ust/cbpmanager", "_realowner": "bioc", "_cranurl": false, "_exports": [ "cbpManager", "setupConda_cbpManager" ], "_help": [ { "page": "addColumn_Server", "title": "Server logic of module for adding a column", "topics": [ "addColumn_Server" ] }, { "page": "addColumn_UI", "title": "UI elements of module for adding a column", "topics": [ "addColumn_UI" ] }, { "page": "addRow_Server", "title": "Server logic of module for adding a row", "topics": [ "addRow_Server" ] }, { "page": "addRow_UI", "title": "UI elements of module for adding a row", "topics": [ "addRow_UI" ] }, { "page": "addRowRc_Server", "title": "Server logic of Resource tab module for adding a row", "topics": [ "addRowRc_Server" ] }, { "page": "addRowRc_UI", "title": "UI elements of Resource tab module for adding a row", "topics": [ "addRowRc_UI" ] }, { "page": "cBioPortalToDataFrame", "title": "Convert the cBioPortal sample- and patient-data file format into a data.frame", "topics": [ "cBioPortalToDataFrame" ] }, { "page": "cbpManager", "title": "Launch cbpManager", "topics": [ "cbpManager" ] }, { "page": "cbpManager-pkg", "title": "cbpManager", "topics": [ "cbpManager-pkg" ] }, { "page": "check_input_dates", "title": "Check the input of dates", "topics": [ "check_input_dates" ] }, { "page": "convertDataFrame", "title": "Convert the data.frame to the appropriate file format for cBioPortal", "topics": [ "convertDataFrame" ] }, { "page": "create_name", "title": "Sanitize names", "topics": [ "create_name" ] }, { "page": "deleteColumn_Server", "title": "Server logic of module for deleting a column", "topics": [ "deleteColumn_Server" ] }, { "page": "deleteColumn_UI", "title": "UI elements of module for deleting a column", "topics": [ "deleteColumn_UI" ] }, { "page": "deleteRow_Server", "title": "Server logic of module for removing a row", "topics": [ "deleteRow_Server" ] }, { "page": "deleteRow_UI", "title": "UI elements of module for removing a row", "topics": [ "deleteRow_UI" ] }, { "page": "deleteRowRc_Server", "title": "Server logic of Resource tab module for deleting a row", "topics": [ "deleteRowRc_Server" ] }, { "page": "deleteRowRc_UI", "title": "UI elements of module for removing a row", "topics": [ "deleteRowRc_UI" ] }, { "page": "editRow_Server", "title": "Server logic of module for editing a row", "topics": [ "editRow_Server" ] }, { "page": "editRow_UI", "title": "UI elements of module for editing a row", "topics": [ "editRow_UI" ] }, { "page": "editRowRc_Server", "title": "Server logic of Resource tab module for editing a row", "topics": [ "editRowRc_Server" ] }, { "page": "editRowRc_UI", "title": "UI elements of module for editing a row", "topics": [ "editRowRc_UI" ] }, { "page": "fncols", "title": "Add empty column to a data.frame, if column does not exist in the data.frame", "topics": [ "fncols" ] }, { "page": "generateOncotreeUIwidgets", "title": "Create shiny UI-widget for specific columns of oncotree entries", "topics": [ "generateOncotreeUIwidgets" ] }, { "page": "generateUIwidgets", "title": "Generate UI input widget", "topics": [ "generateUIwidgets" ] }, { "page": "getSampleIDs", "title": "Get Sample IDs associated with Patient IDs from the data_clinical_sample.txt file", "topics": [ "getSampleIDs" ] }, { "page": "importPatientData", "title": "Import patient data into current study data.frames", "topics": [ "importPatientData" ] }, { "page": "IsDate", "title": "Check if input is in the appropriate date format", "topics": [ "IsDate" ] }, { "page": "saveResource_Server", "title": "Server logic of module for saving the resource data", "topics": [ "saveResource_Server" ] }, { "page": "saveResource_UI", "title": "UI elements of module for saving the resource data", "topics": [ "saveResource_UI" ] }, { "page": "saveTimeline_Server", "title": "Server logic of module for saving the source data", "topics": [ "saveTimeline_Server" ] }, { "page": "saveTimeline_UI", "title": "UI elements of module for saving the data", "topics": [ "saveTimeline_UI" ] }, { "page": "setupConda_cbpManager", "title": "Install conda environment with basilisk before launching the app", "topics": [ "setupConda_cbpManager" ] }, { "page": "shinyAppServer", "title": "Shiny app server function", "topics": [ "shinyAppServer" ] }, { "page": "shinyAppUI", "title": "Shiny app server object create the shiny application user interface", "topics": [ "shinyAppUI" ] }, { "page": "updateOncotreeUIwidgets", "title": "Updates UI-widgets for specific columns of oncotree entries", "topics": [ "updateOncotreeUIwidgets" ] }, { "page": "validateResourceDefinition", "title": "Validate resource_definition input", "topics": [ "validateResourceDefinition" ] }, { "page": "validateResourcePatient", "title": "Validate resource_patient input", "topics": [ "validateResourcePatient" ] }, { "page": "validateResourceSample", "title": "Validate resource_sample input", "topics": [ "validateResourceSample" ] }, { "page": "validateResourceStudy", "title": "Validate resource_study input", "topics": [ "validateResourceStudy" ] }, { "page": "ValidationDependencies", "title": "Validation Dependencies", "topics": [ ".validation_dependencies", "ValidationDependencies" ] }, { "page": "writeLogfile", "title": "Write a line to a logfile containing the date, time, username (from Shinyproxy), and the name of the modified file.", "topics": [ "writeLogfile" ] } ], "_readme": "https://github.com/bioc/cbpManager/raw/HEAD/README.md", "_rundeps": [ "base64enc", "basilisk", "bit", "bit64", "bslib", "cachem", "cli", "commonmark", "cpp11", "crayon", "crosstalk", "digest", "dir.expiry", "dplyr", "DT", "evaluate", "fastmap", "filelock", "fontawesome", "fs", "generics", "glue", "here", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "jquerylib", "jsonlite", "knitr", "later", "lattice", "lazyeval", "lifecycle", "litedown", "magrittr", "markdown", "MASS", "Matrix", "memoise", "mime", "otel", "pander", "pillar", "pkgconfig", "plyr", "png", "prettyunits", "progress", "promises", "R6", "rappdirs", "rapportools", "Rcpp", "RcppTOML", "reshape2", "reticulate", "rintrojs", "rlang", "rmarkdown", "rprojroot", "sass", "shiny", "shinyBS", "shinycssloaders", "shinydashboard", "sourcetools", "stringi", "stringr", "tibble", "tidyselect", "tinytex", "tzdb", "utf8", "vctrs", "vroom", "withr", "xfun", "xtable", "yaml" ], "_vignettes": [ { "source": "intro.rmd", "filename": "intro.html", "title": "cbpManager: Managing cancer studies and generating files for cBioPortal", "author": "Arsenij Ustjanzew", "engine": "knitr::rmarkdown", "headings": [ "Introduction and scope", "Installation", "Installation of the R package", "Docker deployment", "Functionality", "File naming convention", "Editing studies:", "Creating a new study:", "Loading an existing study:", "Editing patient data:", "Add new attributes (columns):", "Create new patients:", "Deleting attributes:", "Import of patients:", "Deleting a patient:", "Saving the patient data:", "Editing sample data:", "Mutation data (MAF):", "Editing timelines:", "Manage resources data:", "Validating created study", "Upload to cBioPortal for Cancer Genomics.", "Session Info" ], "created": "2021-01-12 10:41:13", "modified": "2021-11-26 12:34:23", "commits": 8 } ], "_score": 5.505149978319906, "_indexed": true, "_nocasepkg": "cbpmanager", "_universes": [ "bioc", "arsenij-ust" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-05-30T09:54:07.000Z", "distro": "noble", "commit": "f2bfaa697f1902924f2dee4dbde49fdfe236a80c", "fileid": "721efeaf5dd4ae9ebadce327fa1dc988da1f885c9a361ad6a25b1ae0cdca2413", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676150350" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-05-30T09:54:37.000Z", "distro": "noble", "commit": "f2bfaa697f1902924f2dee4dbde49fdfe236a80c", "fileid": "06ac94365bc9864f9b37614c0fc51bc0ec5912bd04cdeeb58d398f43da195de4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676150350" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-05-30T13:34:01.000Z", "commit": "f2bfaa697f1902924f2dee4dbde49fdfe236a80c", "fileid": "de5a368d98b3c030fa052c1cc3a8444504a16a776c7bf2f4e1ab9e12ada35e7f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676150350" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-05-30T13:33:17.000Z", "commit": "f2bfaa697f1902924f2dee4dbde49fdfe236a80c", "fileid": "6542303231546eae2ed3333b5a64cd0688a58f76d4aab0d35c5438a5b331067b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676150350" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-05-30T09:54:20.000Z", "commit": "f2bfaa697f1902924f2dee4dbde49fdfe236a80c", "fileid": "a10c441159847592f6ce12815e3b51048e33e708712fb367a6d7ad4eb1e0e34a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676150350" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-05-30T09:53:25.000Z", "commit": "f2bfaa697f1902924f2dee4dbde49fdfe236a80c", "fileid": "21355d91b26cdafb140e00c85221428f3c2d9fc6504cb5d10958027162d81a76", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676150350" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-05-30T09:53:13.000Z", "commit": "f2bfaa697f1902924f2dee4dbde49fdfe236a80c", "fileid": "7ee0b54ae2b0a0f720e71b709f38a3f0bf42b4d960016e70908318d21e83d391", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676150350" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-05-30T09:53:23.000Z", "commit": "f2bfaa697f1902924f2dee4dbde49fdfe236a80c", "fileid": "ccf40dcb62999505993eac7e416eae28ff39943dbf898904f0f8a2e884ac59e0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676150350" } ] }