{ "_id": "6accc305a14063b82c3a8d2a", "Package": "VegaMC", "Type": "Package", "Title": "VegaMC: A Package Implementing a Variational Piecewise Smooth\nModel for Identification of Driver Chromosomal Imbalances in\nCancer", "Version": "3.50.0", "Date": "2015-03-03", "Author": "S. Morganella and M. Ceccarelli", "Maintainer": "Sandro Morganella ", "Description": "This package enables the detection of driver chromosomal\nimbalances including loss of heterozygosity (LOH) from array\ncomparative genomic hybridization (aCGH) data. VegaMC performs\na joint segmentation of a dataset and uses a statistical\nframework to distinguish between driver and passenger mutation.\nVegaMC has been implemented so that it can be immediately\nintegrated with the output produced by PennCNV tool. In\naddition, VegaMC produces in output two web pages that allows a\nrapid navigation between both the detected regions and the\naltered genes. In the web page that summarizes the altered\ngenes, the link to the respective Ensembl gene web page is\nreported.", "License": "GPL-2", "LazyLoad": "yes", "biocViews": "aCGH, CopyNumberVariation", "Packaged": { "Date": "2026-10-12 11:17:32 UTC", "User": "root" }, "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:36:23 UTC", "RemoteUrl": "https://github.com/bioc/VegaMC", "RemoteRef": "RELEASE_3_23", "RemoteSha": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "NeedsCompilation": "yes", "_user": "bioc-release", "_type": "src", "_file": "VegaMC_3.50.0.tar.gz", "_fileid": "https://r2.ropensci.org/3d8b6efbc0e0f9dab22c9854ac52d672eee1760776a324ca65f12700b141e4e1", "_filesize": 1914564, "_sha256": "3d8b6efbc0e0f9dab22c9854ac52d672eee1760776a324ca65f12700b141e4e1", "_expires": "2027-01-20T11:22:43.000Z", "_created": "2026-10-12T11:17:32.000Z", "_published": "2026-10-12T11:22:45.595Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 1, "warning": 3, "note": 13 }, "_upstream": "https://github.com/bioc/VegaMC", "_commit": { "id": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379783 }, "_maintainer": { "name": "Sandro Morganella", "email": "morganellaalx@gmail.com", "login": "smorganella", "description": "", "uuid": 15774169 }, "_distro": "resolute", "_jobs": [ { "job": 114785802877, "time": 140, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11743785195" }, { "job": 114785803075, "time": 160, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "11743215995" }, { "job": 114785803118, "time": 259, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11744130030" }, { "job": 114785803035, "time": 126, "config": "linux-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11743250765" }, { "job": 114785803162, "time": 255, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11743361034" }, { "job": 114785802983, "time": 126, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11743585319" }, { "job": 114785802945, "time": 260, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11743425979" }, { "job": 114785802984, "time": 162, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11743138393" }, { "job": 114785802979, "time": 263, "config": "macos-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11743465854" }, { "job": 114784166696, "time": 274, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11743089155" }, { "job": 114785802798, "time": 100, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11743690162" }, { "job": 114785803231, "time": 252, "config": "windows-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "11743226265" }, { "job": 114785803045, "time": 137, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11743260869" }, { "job": 114785803286, "time": 116, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11743270734" }, { "job": 114785803230, "time": 235, "config": "windows-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11743815423" }, { "job": 114785803194, "time": 142, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11743705268" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10.0", "role": "Depends" }, { "package": "biomaRt", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "methods", "role": "Imports" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "3.51.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "3.50.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "acgh", "copynumbervariation" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 546, "source": "https://www.bioconductor.org/packages/stats/bioc/VegaMC" }, "_mentions": 2, "_searchresults": 1, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/VegaMC.html" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "sortData", "vegaMC" ], "_help": [ { "page": "VegaMC-package", "title": "VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer.", "topics": [ "VegaMC-package", "VegaMC" ] }, { "page": "sortData", "title": "This function sorts a dataset file by the genomic position of the probes.", "topics": [ "sortData" ] }, { "page": "vegaMC-methods", "title": "Class aggregator of VegaMC.", "topics": [ "vegaMC", "vegaMC,character-method", "vegaMC-methods" ] } ], "_rundeps": [ "AnnotationDbi", "askpass", "Biobase", "BiocFileCache", "BiocGenerics", "biomaRt", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "dbplyr", "dplyr", "fastmap", "filelock", "generics", "glue", "hms", "httr", "httr2", "IRanges", "jsonlite", "KEGGREST", "lifecycle", "magrittr", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "xml2", "XVector" ], "_vignettes": [ { "source": "VegaMC.Rnw", "filename": "VegaMC.pdf", "title": "VegaMC", "engine": "utils::Sweave", "headings": [ "1 Overview", "2 Installation and Dependencies", "3 Input Data Format", "4 VegaMC", "5 VegaMC: Run Analysis", "6 Analysis of Gastrointestinal Stromal Tumors (GIST) Dataset" ], "created": "2013-11-01 20:24:43", "modified": "2018-09-06 15:53:21", "commits": 4 } ], "_score": 3.6020599913279625, "_indexed": false, "_nocasepkg": "vegamc", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/VegaMC", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.50.0", "date": "2026-10-12T11:19:34.000Z", "distro": "resolute", "arch": "aarch64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/a450ed4daf7fadc67d9bc795c15e0e659ee07c7770a1a35425859a6e7d779793", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.7.0", "os": "linux", "version": "3.50.0", "date": "2026-10-12T11:21:12.000Z", "distro": "resolute", "arch": "x86_64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/c34e7b4dd89ca3855788cd25554538053dc0353f5e8e081e517f656d975eb381", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.6.1", "os": "linux", "version": "3.50.0", "date": "2026-10-12T11:19:26.000Z", "distro": "resolute", "arch": "aarch64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/166456ce71b5a79cf91a0a242b899e94e669e2232b2eff47a2638ad4e859d36c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.6.1", "os": "linux", "version": "3.50.0", "date": "2026-10-12T11:20:59.000Z", "distro": "resolute", "arch": "x86_64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/a6f893e2c644ffc5d02f27040be9a239e0a463c615720ead0f2c7ff8b268a4bf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.5.3", "os": "mac", "version": "3.50.0", "date": "2026-10-12T11:19:13.000Z", "arch": "aarch64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/a70e743436ea47faacfe2476ec161046390f0dc8f6a7d0f5aa175d4aa7d57bbd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.5.3", "os": "mac", "version": "3.50.0", "date": "2026-10-12T11:20:41.000Z", "arch": "x86_64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/f2ccb9551bdbd663d29a0770f46c45444989fec86787c5565bf06a99de779b4c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.6.1", "os": "mac", "version": "3.50.0", "date": "2026-10-12T11:19:39.000Z", "arch": "aarch64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/4fab202b6f16bc8c04bb52aeeaf4c3477eebee12ee0665920864dba5b0c79242", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.6.1", "os": "mac", "version": "3.50.0", "date": "2026-10-12T11:20:26.000Z", "arch": "x86_64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/e64346e2bd8f521eab6d71c2e6b67352a1708c895b78bf191f674167cf53db34", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.6.0", "os": "wasm", "version": "3.50.0", "date": "2026-10-12T11:19:31.000Z", "arch": "emscripten", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/a64ba1c559f7196edbb3b11d585ac748d10456415f3d31e7f1cc77a890c88f87", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.7.0", "os": "win", "version": "3.50.0", "date": "2026-10-12T11:20:45.000Z", "arch": "aarch64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/3b8a965e96c2e0a8fc63df98075fb64c5dbbca95bc475e23d2184f4e88e4c113", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.7.0", "os": "win", "version": "3.50.0", "date": "2026-10-12T11:18:39.000Z", "arch": "x86_64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/94c90a67208adc8203c409f9cea3d047867383a49ef4ef251953d40250449507", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.5.3", "os": "win", "version": "3.50.0", "date": "2026-10-12T11:18:38.000Z", "arch": "x86_64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/800d9687257ff20fc1e2c783161590c4d3509cd1be353f7563d7ad62b642657f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.6.1", "os": "win", "version": "3.50.0", "date": "2026-10-12T11:20:37.000Z", "arch": "aarch64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/dd841ab4ed91c640889f800ae78895f28df29777a0101645fbc494fcddf2bd3c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" }, { "r": "4.6.1", "os": "win", "version": "3.50.0", "date": "2026-10-12T11:18:49.000Z", "arch": "x86_64", "commit": "1b6044b63d0ed59ee7002854a07c6edf9024c94b", "fileid": "https://r2.ropensci.org/020ab2a2113ee36247ec05838528286aa2998825564cef6e36c5d20c6c489d4d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241216097" } ] }