{ "_id": "6a1aeb491d7bb097a09f3c79", "Package": "timescape", "Title": "Patient Clonal Timescapes", "Version": "1.37.0", "Authors@R": "person(\"Maia\", \"Smith\", email = \"maiaannesmith@gmail.com\", role = c(\"aut\", \"cre\"))", "Description": "TimeScape is an automated tool for navigating temporal\nclonal evolution data. The key attributes of this\nimplementation involve the enumeration of clones, their\nevolutionary relationships and their shifting dynamics over\ntime. TimeScape requires two inputs: (i) the clonal phylogeny\nand (ii) the clonal prevalences. Optionally, TimeScape accepts\na data table of targeted mutations observed in each clone and\ntheir allele prevalences over time. The output is the TimeScape\nplot showing clonal prevalence vertically, time horizontally,\nand the plot height optionally encoding tumour volume during\ntumour-shrinking events. At each sampling time point (denoted\nby a faint white line), the height of each clone accurately\nreflects its proportionate prevalence. These prevalences form\nthe anchors for bezier curves that visually represent the\ndynamic transitions between time points.", "biocViews": "Visualization, BiomedicalInformatics", "License": "GPL-3", "RoxygenNote": "6.0.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:45:09 UTC", "RemoteUrl": "https://github.com/bioc/timescape", "RemoteRef": "HEAD", "RemoteSha": "b0f7631ab5919eaec4e5b4f48d0217d916f8abc9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:40:28 UTC", "User": "root" }, "Author": "Maia Smith [aut, cre]", "Maintainer": "Maia Smith ", "MD5sum": "d00dfc6f79533b0da3966a7697dab8ae", "_user": "bioc", "_type": "src", "_file": "timescape_1.37.0.tar.gz", "_fileid": "60aa49613f7943775d7507b9d02867445516ec4c28e747048f0dc6000ef2c96f", "_filesize": 563410, "_sha256": "60aa49613f7943775d7507b9d02867445516ec4c28e747048f0dc6000ef2c96f", "_created": "2026-05-30T09:40:28.000Z", "_published": "2026-05-30T13:51:05.948Z", "_jobs": [ { "job": 78640269513, "time": 146, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307372438" }, { "job": 78640269503, "time": 138, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307369431" }, { "job": 78640269495, "time": 171, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307373212" }, { "job": 78640269497, "time": 79, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308646218" }, { "job": 78640269498, "time": 93, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308646501" }, { "job": 78639701006, "time": 163, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307248277" }, { "job": 78640269486, "time": 108, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307366445" }, { "job": 78640269501, "time": 77, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307364377" }, { "job": 78640269502, "time": 76, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307364307" }, { "job": 78640269500, "time": 85, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307365536" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676545322", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/timescape", "_commit": { "id": "b0f7631ab5919eaec4e5b4f48d0217d916f8abc9", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380309 }, "_maintainer": { "name": "Maia Smith", "email": "maiaannesmith@gmail.com", "login": "maiasmith", "description": "", "uuid": 18253994 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3", "role": "Depends" }, { "package": "htmlwidgets", "version": ">= 0.5", "role": "Imports" }, { "package": "jsonlite", "version": ">= 0.9.19", "role": "Imports" }, { "package": "stringr", "version": ">= 1.0.0", "role": "Imports" }, { "package": "dplyr", "version": ">= 0.4.3", "role": "Imports" }, { "package": "gtools", "version": ">= 3.5.0", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.37.0", "bioc": "3.24" }, { "branch": "release", "version": "1.36.0", "bioc": "3.23" } ], "_topics": [ "visualization", "biomedicalinformatics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 352, "source": "https://www.bioconductor.org/packages/stats/bioc/timescape" }, "_mentions": 1, "_searchresults": 13, "_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/timescape.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "checkAlpha", "checkClonalPrev", "checkCloneColours", "checkGtypePositioning", "checkMinDims", "checkPerts", "checkRequiredInputs", "checkTreeEdges", "getMutationsData", "processUserData", "renderTimescape", "replaceSpaces", "timescape", "timescapeOutput" ], "_help": [ { "page": "timescape", "title": "TimeScape", "topics": [ "timescape" ] }, { "page": "helpers", "title": "Widget output function for use in Shiny", "topics": [ "checkAlpha", "checkClonalPrev", "checkCloneColours", "checkGtypePositioning", "checkMinDims", "checkPerts", "checkRequiredInputs", "checkTreeEdges", "getMutationsData", "processUserData", "renderTimescape", "replaceSpaces", "timescapeOutput" ] } ], "_readme": "https://github.com/bioc/timescape/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bslib", "cachem", "cli", "digest", "dplyr", "evaluate", "fastmap", "fontawesome", "fs", "generics", "glue", "gtools", "highr", "htmltools", "htmlwidgets", "jquerylib", "jsonlite", "knitr", "lifecycle", "magrittr", "memoise", "mime", "pillar", "pkgconfig", "R6", "rappdirs", "rlang", "rmarkdown", "sass", "stringi", "stringr", "tibble", "tidyselect", "tinytex", "utf8", "vctrs", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "timescape_vignette.Rmd", "filename": "timescape_vignette.html", "title": "TimeScape vignette", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Examples", "Required parameters", "Optional parameters", "Mutations", "Clone colours", "Alpha value", "Titles", "Genotype position", "Stacked", "Spaced", "Centered", "Perturbation events", "Without perturbation", "With perturbation", "Obtaining the data", "Interactivity", "Documentation", "References" ], "created": "2017-02-11 19:22:18", "modified": "2018-08-30 17:57:40", "commits": 4 } ], "_score": 4.113943352306837, "_indexed": true, "_nocasepkg": "timescape", "_universes": [ "bioc", "maiasmith" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.37.0", "date": "2026-05-30T10:01:04.000Z", "distro": "noble", "commit": "b0f7631ab5919eaec4e5b4f48d0217d916f8abc9", "fileid": "d49fe40478679b481068813130d9e17ba022c217d31cfcda101b48ad9e57220e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676545322" }, { "r": "4.6.0", "os": "linux", "version": "1.37.0", "date": "2026-05-30T10:01:45.000Z", "distro": "noble", "commit": "b0f7631ab5919eaec4e5b4f48d0217d916f8abc9", "fileid": "1a4008b3c50dc287c6f1e546bc31a98c5d3544954735b990a5add1db447ef14b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676545322" }, { "r": "4.5.3", "os": "mac", "version": "1.37.0", "date": "2026-05-30T13:50:35.000Z", "commit": "b0f7631ab5919eaec4e5b4f48d0217d916f8abc9", "fileid": "a8bd80028be5c9e56fdd2cb640fa976cd44a844c8674f7687a193f51d7d1fdbe", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676545322" }, { "r": "4.6.0", "os": "mac", "version": "1.37.0", "date": "2026-05-30T13:50:38.000Z", "commit": "b0f7631ab5919eaec4e5b4f48d0217d916f8abc9", "fileid": "6c099b83d1df0af535090d326bff20ffa64ce7f773869b4102adfa481ccdf9ed", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676545322" }, { "r": "4.6.0", "os": "wasm", "version": "1.37.0", "date": "2026-05-30T10:00:45.000Z", "commit": "b0f7631ab5919eaec4e5b4f48d0217d916f8abc9", "fileid": "a3fa4205ca359d2fb9a8fbe7320d75dff044366c65b3bf35f8e0f67d1644e1a1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676545322" }, { "r": "4.7.0", "os": "win", "version": "1.37.0", "date": "2026-05-30T10:00:09.000Z", "commit": "b0f7631ab5919eaec4e5b4f48d0217d916f8abc9", "fileid": "263e8b76274e62c145a6b00ef05aae3ea1f11d7531c6ccc8efc82ffcd198202d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676545322" }, { "r": "4.5.3", "os": "win", "version": "1.37.0", "date": "2026-05-30T10:00:05.000Z", "commit": "b0f7631ab5919eaec4e5b4f48d0217d916f8abc9", "fileid": "db052eb810a563e2889b669078d87d9f398d84a0941fbaddf2cb67a8dc95cf54", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676545322" }, { "r": "4.6.0", "os": "win", "version": "1.37.0", "date": "2026-05-30T10:00:19.000Z", "commit": "b0f7631ab5919eaec4e5b4f48d0217d916f8abc9", "fileid": "c296a05f5ded2b9519e4231e3f10e1fce60fa82d0e8be86dd3a6130870cb030a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676545322" } ] }