{ "_id": "6ae856551e2c7b3a4f5317dd", "Package": "Clomial", "Type": "Package", "Title": "Infers clonal composition of a tumor", "Version": "1.49.0", "Date": "2018-05-31", "Author": "Habil Zare and Alex Hu", "Maintainer": "Habil Zare ", "Description": "Clomial fits binomial distributions to counts obtained\nfrom Next Gen Sequencing data of multiple samples of the same\ntumor. The trained parameters can be interpreted to infer the\nclonal structure of the tumor.", "License": "GPL (>= 2)", "biocViews": "Genetics, GeneticVariability, Sequencing, Clustering,\nMultipleComparison, Bayesian, DNASeq, ExomeSeq,\nTargetedResequencing, ImmunoOncology", "LazyLoad": "yes", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:38:42 UTC", "RemoteUrl": "https://github.com/bioc/Clomial", "RemoteRef": "HEAD", "RemoteSha": "ca3ec4d09c62e776f17f5636e27a4671de335643", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-02 08:05:06 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "Clomial_1.49.0.tar.gz", "_fileid": "https://r2.ropensci.org/b517b34e1eb3ded1924b0214f0627df03edb08cff036099fdab18ad76c1dae44", "_filesize": 1546028, "_sha256": "b517b34e1eb3ded1924b0214f0627df03edb08cff036099fdab18ad76c1dae44", "_expires": "2027-02-10T09:22:27.000Z", "_created": "2026-11-02T08:05:06.000Z", "_published": "2026-11-02T09:22:29.159Z", "_upstream": "https://github.com/bioc/Clomial", "_status": "success", "_maintainer": { "name": "Habil Zare", "email": "zare@u.washington.edu" }, "_jobs": [ { "job": 125162251009, "time": 169, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13124914180" }, { "job": 125162251006, "time": 231, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13124694000" }, { "job": 125162251028, "time": 232, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13124759956" }, { "job": 125162251047, "time": 151, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "13128284598" }, { "job": 125162251074, "time": 135, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13128963677" }, { "job": 125161240696, "time": 168, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13125292403" }, { "job": 125162251031, "time": 89, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13125785484" }, { "job": 125162251049, "time": 115, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13125950983" }, { "job": 125162250905, "time": 137, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13125760836" }, { "job": 125162251016, "time": 132, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13124714597" } ], "_bioccheck": { "error": 2, "warning": 5, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41410155374", "_commit": { "id": "ca3ec4d09c62e776f17f5636e27a4671de335643", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379922 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "matrixStats", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "permute", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.49.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.48.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "genetics", "geneticvariability", "sequencing", "clustering", "multiplecomparison", "bayesian", "dnaseq", "exomeseq", "targetedresequencing", "immunooncology" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 483, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 520, "source": "https://www.bioconductor.org/packages/stats/bioc/Clomial" }, "_mentions": 10, "_searchresults": 3, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/Clomial.html", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "choose.best", "Clomial", "Clomial.generate.data", "Clomial.iterate", "Clomial.likelihood", "compute.bic", "compute.errors" ], "_datasets": [ { "name": "breastCancer", "title": "Breast cancer data for clonal decomposition.", "object": "breastCancer", "file": "breastCancer.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "Clomial1000", "title": "Pre-computed results of Clomial.", "object": "Clomial1000", "file": "Clomial1000.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "Clomial-package", "title": "Fits a binomial model to data from multiple samples of a single tumor to infer its clonal decomposition.", "topics": [ "Clomial-package" ] }, { "page": "breastCancer", "title": "Breast cancer data for clonal decomposition.", "topics": [ "breastCancer" ] }, { "page": "choose.best", "title": "Chooses the best trained Clomial model.", "topics": [ "choose.best" ] }, { "page": "Clomial", "title": "Fits several binomial models to data from multiple samples of a single tumor.", "topics": [ "Clomial" ] }, { "page": "Clomial.generate.data", "title": "Generates simulated data to test performance of Clomial algorithm.", "topics": [ "Clomial.generate.data" ] }, { "page": "Clomial.iterate", "title": "Runs EM iterations until convergence of the Clomial model.", "topics": [ "Clomial.iterate" ] }, { "page": "Clomial.likelihood", "title": "Computes the complete data log-likelihood of a Clomial model.", "topics": [ "Clomial.likelihood" ] }, { "page": "Clomial1000", "title": "Pre-computed results of Clomial.", "topics": [ "Clomial1000" ] }, { "page": "compute.bic", "title": "Computes BIC for a Clomial model.", "topics": [ "compute.bic" ] }, { "page": "compute.errors", "title": "Computes the error of a Clomial model.", "topics": [ "compute.errors" ] } ], "_rundeps": [ "matrixStats", "permute" ], "_vignettes": [ { "source": "Clonal_decomposition_by_Clomial.Rnw", "filename": "Clonal_decomposition_by_Clomial.pdf", "title": "A likelihood maximization approach to infer the clonal structure of a cancer using multiple tumor samples", "engine": "utils::Sweave", "headings": [ "Introduction", "How to run Clomial?", "Reference" ], "created": "2014-03-10 20:31:51", "modified": "2021-02-10 17:02:51", "commits": 7 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "clomial", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.49.0", "date": "2026-11-02T08:08:10.000Z", "distro": "resolute", "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643", "fileid": "https://r2.ropensci.org/3fbcf179e7b8fd22c933bb2f0cff93b36ed5ae30a9f45deb60944a9686390cb4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41410155374" }, { "r": "4.6.2", "os": "linux", "version": "1.49.0", "date": "2026-11-02T08:08:37.000Z", "distro": "resolute", "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643", "fileid": "https://r2.ropensci.org/a1848737755a6a4f9da117d21d274c6e7372cff317603c07bd142ff0a11b6435", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41410155374" }, { "r": "4.5.3", "os": "mac", "version": "1.49.0", "date": "2026-11-02T09:19:07.000Z", "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643", "fileid": "https://r2.ropensci.org/33ce0ef63e22f1be18f729f4c65d82a92d6edeebcfa617e6ccf06b70218ce434", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41410155374" }, { "r": "4.6.2", "os": "mac", "version": "1.49.0", "date": "2026-11-02T09:21:07.000Z", "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643", "fileid": "https://r2.ropensci.org/18e3c9d75e4437703b3f627fbc0ee536d98ad4d849bbd3baffbf16ac6ae30bb9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41410155374" }, { "r": "4.6.0", "os": "wasm", "version": "1.49.0", "date": "2026-11-02T08:06:45.000Z", "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643", "fileid": "https://r2.ropensci.org/3bfefab6e5892d7cb42c30363bb83e9991baaa6616ccdb75358dbba152ebc926", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41410155374" }, { "r": "4.7.0", "os": "win", "version": "1.49.0", "date": "2026-11-02T08:06:10.000Z", "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643", "fileid": "https://r2.ropensci.org/0862da1af5f280b0cd54e4d07e539a2706a88a20f91f036f1a93789730492467", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41410155374" }, { "r": "4.5.3", "os": "win", "version": "1.49.0", "date": "2026-11-02T08:06:17.000Z", "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643", "fileid": "https://r2.ropensci.org/3a7f850f30ae6aa1f79bc1de08fe3ea44098494ad029e792349949fbc42d3671", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41410155374" }, { "r": "4.6.2", "os": "win", "version": "1.49.0", "date": "2026-11-02T08:06:09.000Z", "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643", "fileid": "https://r2.ropensci.org/11d64f58f650d3ee2ae1073861b82f029787fa52d98ed70823f533cd9da97ae0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41410155374" } ] }