{ "_id": "6a1ac1051d7bb097a09d7511", "Package": "oncoscanR", "Type": "Package", "Title": "Secondary analyses of CNV data (HRD and more)", "Version": "1.15.0", "Authors@R": "c(person(\"Yann\", \"Christinat\", email = \"yann.christinat@hcuge.ch\", \nrole = c(\"aut\", \"cre\")),\nperson(\"Geneva University Hospitals\", role=c(\"aut\", \"cph\")))", "Description": "The software uses the copy number segments from a text\nfile and identifies all chromosome arms that are globally\naltered and computes various genome-wide scores. The following\nHRD scores (characteristic of BRCA-mutated cancers) are\nincluded: LST, HR-LOH, nLST and gLOH. the package is tailored\nfor the ThermoFisher Oncoscan assay analyzed with their\nChromosome Alteration Suite (ChAS) but can be adapted to any\ninput.", "License": "MIT + file LICENSE", "Date": "2025-06-27", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "biocViews": "CopyNumberVariation, Microarray, Software", "RoxygenNote": "7.3.2", "URL": "https://github.com/yannchristinat/oncoscanR", "BugReports": "https://github.com/yannchristinat/oncoscanR/issues", "LazyData": "true", "Config/pak/sysreqs": "libx11-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:48 UTC", "RemoteUrl": "https://github.com/bioc/oncoscanR", "RemoteRef": "HEAD", "RemoteSha": "74407d7cd88ef1665e19c7847bbe2bbf79a6fc40", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:18:41 UTC", "User": "root" }, "Author": "Yann Christinat [aut, cre],\nGeneva University Hospitals [aut, cph]", "Maintainer": "Yann Christinat ", "MD5sum": "b1aacdb83ca8651b105d33409428ba1b", "_user": "bioc", "_type": "src", "_file": "oncoscanR_1.15.0.tar.gz", "_fileid": "b3fae1119be05f522d7f0f4ddf40438b455b15778cd9296f86f30319b37140bf", "_filesize": 948897, "_sha256": "b3fae1119be05f522d7f0f4ddf40438b455b15778cd9296f86f30319b37140bf", "_created": "2026-05-30T07:18:41.000Z", "_published": "2026-05-30T10:50:45.547Z", "_jobs": [ { "job": 78633009112, "time": 160, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306424044" }, { "job": 78633009117, "time": 318, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7306440522" }, { "job": 78633009116, "time": 330, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7306441755" }, { "job": 78633009125, "time": 247, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7307544878" }, { "job": 78633009114, "time": 198, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7307538662" }, { "job": 78632755053, "time": 283, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306405582" }, { "job": 78633009103, "time": 115, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306419199" }, { "job": 78633009122, "time": 284, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7306436838" }, { "job": 78633009119, "time": 318, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7306440351" }, { "job": 78633009123, "time": 178, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7306425836" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677790983", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/oncoscanR", "_commit": { "id": "74407d7cd88ef1665e19c7847bbe2bbf79a6fc40", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381128 }, "_maintainer": { "name": "Yann Christinat", "email": "yann.christinat@hcuge.ch", "login": "yannchristinat", "description": "Clinical bioinformatics", "uuid": 29749799 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "IRanges", "version": ">= 2.30.0", "role": "Depends" }, { "package": "GenomicRanges", "version": ">= 1.48.0", "role": "Depends" }, { "package": "magrittr", "role": "Depends" }, { "package": "readr", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "version": ">= 3.1.4", "role": "Suggests" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.15.0", "bioc": "3.24" }, { "branch": "release", "version": "1.14.0", "bioc": "3.23" } ], "_topics": [ "copynumbervariation", "microarray", "software" ], "_stars": 3, "_contributors": [ { "user": "yannchristinat", "count": 78, "uuid": 29749799 }, { "user": "jwokaty", "count": 8, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 319, "source": "https://www.bioconductor.org/packages/stats/bioc/oncoscanR" }, "_devurl": "https://github.com/yannchristinat/oncoscanr", "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/oncoscanR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/yannchristinat/oncoscanr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "adjust_loh", "armlevel_alt", "get_amp_segments", "get_gain_segments", "get_hetloss_segments", "get_homloss_segments", "get_loh_segments", "get_loss_segments", "get_oncoscan_coverage_from_bed", "load_ascat", "load_chas", "merge_segments", "prune_by_size", "score_avgcn", "score_estwgd", "score_gloh", "score_loh", "score_lst", "score_mbalt", "score_nlst", "score_td", "trim_to_coverage", "workflow_oncoscan.ascat", "workflow_oncoscan.chas" ], "_datasets": [ { "name": "cntypes", "title": "Accepted types of CN for the segments - 'Gain': 1-2 extra copies - 'Weak amplification': 3-7 extra copies - 'Strong amplification': 8 or more extra copies - 'Heterozygote loss': Loss of one copy out of two - 'Homozygote loss': Loss of all copies - 'LOH': copy-neutral loss of one parental allele", "object": "cntypes", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "oncoscan_na33.cov", "title": "GenomicRanges object of the chromosomal arms coverage for the oncoscan assay (based on file extdata/Oncoscan.na33.r2.cov.processed.bed).", "object": "oncoscan_na33.cov", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "segs.chas_example", "title": "Expected segments from loading the ChAS file 'chas_example.txt'.", "object": "segs.chas_example", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "adjust_loh", "title": "Trim LOH segments with respect to loss segments.", "topics": [ "adjust_loh" ] }, { "page": "armlevel_alt", "title": "Get all globally-altered chromosome arms.", "topics": [ "armlevel_alt" ] }, { "page": "cntypes", "title": "Accepted types of CN for the segments - 'Gain': 1-2 extra copies - 'Weak amplification': 3-7 extra copies - 'Strong amplification': 8 or more extra copies - 'Heterozygote loss': Loss of one copy out of two - 'Homozygote loss': Loss of all copies - 'LOH': copy-neutral loss of one parental allele", "topics": [ "cntypes" ] }, { "page": "get_amp_segments", "title": "Return all segments with an amplification (5 or more copies).", "topics": [ "get_amp_segments" ] }, { "page": "get_gain_segments", "title": "Return all segments with gain of copies.", "topics": [ "get_gain_segments" ] }, { "page": "get_hetloss_segments", "title": "Return all segments with heterozygous loss.", "topics": [ "get_hetloss_segments" ] }, { "page": "get_homloss_segments", "title": "Return all segments with homozygous loss.", "topics": [ "get_homloss_segments" ] }, { "page": "get_loh_segments", "title": "Return all segments of type LOH, independently of the copy number.", "topics": [ "get_loh_segments" ] }, { "page": "get_loss_segments", "title": "Return all segments with loss of 1 or 2 copies.", "topics": [ "get_loss_segments" ] }, { "page": "get_oncoscan_coverage_from_bed", "title": "Load the oncoscan coverage BED file into a GenomicRanges object.", "topics": [ "get_oncoscan_coverage_from_bed" ] }, { "page": "load_ascat", "title": "Load am ASCAT text export file.", "topics": [ "load_ascat" ] }, { "page": "load_chas", "title": "Load a ChAS text export file.", "topics": [ "load_chas" ] }, { "page": "merge_segments", "title": "Merge segments with respect to the kit resolution and the copy number.", "topics": [ "merge_segments" ] }, { "page": "oncoscan_na33.cov", "title": "GenomicRanges object of the chromosomal arms coverage for the oncoscan assay (based on file extdata/Oncoscan.na33.r2.cov.processed.bed).", "topics": [ "oncoscan_na33.cov" ] }, { "page": "prune_by_size", "title": "Remove segments smaller than the kit resolution.", "topics": [ "prune_by_size" ] }, { "page": "score_avgcn", "title": "Compute the average copy number variation across the genome.", "topics": [ "score_avgcn" ] }, { "page": "score_estwgd", "title": "Estimates the number of whole-genome doubling events (WGD).", "topics": [ "score_estwgd" ] }, { "page": "score_gloh", "title": "Compute the genomic LOH score.", "topics": [ "score_gloh" ] }, { "page": "score_loh", "title": "Compute the number HR deficiency-associated LOH regions.", "topics": [ "score_loh" ] }, { "page": "score_lst", "title": "Compute the number of Large-scale State Transitions (LSTs).", "topics": [ "score_lst" ] }, { "page": "score_mbalt", "title": "Computes the total number of Mbp altered.", "topics": [ "score_mbalt" ] }, { "page": "score_nlst", "title": "Compute the number of LSTs, normalized by the number of WGD events.", "topics": [ "score_nlst" ] }, { "page": "score_td", "title": "Compute the number of large tandem duplication (TDplus).", "topics": [ "score_td" ] }, { "page": "segs.chas_example", "title": "Expected segments from loading the ChAS file 'chas_example.txt'.", "topics": [ "segs.chas_example" ] }, { "page": "trim_to_coverage", "title": "Trim segments with respect to the kit's coverage.", "topics": [ "trim_to_coverage" ] }, { "page": "workflow_oncoscan.ascat", "title": "Run the standard workflow for ASCAT files (from oncoscan data).", "topics": [ "workflow_oncoscan.ascat" ] }, { "page": "workflow_oncoscan.chas", "title": "Run the standard workflow for Oncoscan ChAS files.", "topics": [ "workflow_oncoscan.chas" ] } ], "_readme": "https://github.com/bioc/oncoscanR/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "bit", "bit64", "cli", "clipr", "cpp11", "crayon", "generics", "GenomicRanges", "glue", "hms", "IRanges", "lifecycle", "magrittr", "pillar", "pkgconfig", "prettyunits", "progress", "R6", "readr", "rlang", "S4Vectors", "Seqinfo", "tibble", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr" ], "_vignettes": [ { "source": "oncoscanR.Rmd", "filename": "oncoscanR.html", "title": "Secondary analyses of CNV data (HRD and more) with oncoscanR", "author": "Yann Christinat", "engine": "knitr::rmarkdown", "headings": [ "OncoscanR package description", "Inclusion in Bioconductor", "Getting started", "Installation", "Testing the installation", "Use cases", "Loading a ChAS export file and do a bit of cleaning", "Computation of arm-level alteration", "Global level of alteration", "HRD scores", "Score LST", "Score HR-LOH", "Score nLST", "Score gLOH", "Example", "TDplus score", "Main workflow (as used at the Geneva University Hospitals)", "References", "Session info" ], "created": "2022-04-19 08:58:34", "modified": "2023-04-26 11:14:38", "commits": 10 } ], "_score": 4.653212513775344, "_indexed": true, "_nocasepkg": "oncoscanr", "_universes": [ "bioc", "yannchristinat" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.15.0", "date": "2026-05-30T07:21:05.000Z", "distro": "noble", "commit": "74407d7cd88ef1665e19c7847bbe2bbf79a6fc40", "fileid": "b54c39993ee0c276b20341fbc32e1edc4fbba240ee4a6827e1869766f5b75e85", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677790983" }, { "r": "4.6.0", "os": "linux", "version": "1.15.0", "date": "2026-05-30T07:21:19.000Z", "distro": "noble", "commit": "74407d7cd88ef1665e19c7847bbe2bbf79a6fc40", "fileid": "433ad78f7ebd8873fb3d07f1ad01e7c47524002ef8dafbc91c6ef1bf067883b9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677790983" }, { "r": "4.5.3", "os": "mac", "version": "1.15.0", "date": "2026-05-30T10:31:28.000Z", "commit": "74407d7cd88ef1665e19c7847bbe2bbf79a6fc40", "fileid": "84a67e1da810807eeaa56f5f7afd453113aab6fa805be2b808ce30ba87749e18", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677790983" }, { "r": "4.6.0", "os": "mac", "version": "1.15.0", "date": "2026-05-30T10:31:10.000Z", "commit": "74407d7cd88ef1665e19c7847bbe2bbf79a6fc40", "fileid": "c116ee7fc0adb659c488255da962209662aef00b5b87be0c0ac3c06e5a7f9995", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677790983" }, { "r": "4.6.0", "os": "wasm", "version": "1.15.0", "date": "2026-05-30T07:21:02.000Z", "commit": "74407d7cd88ef1665e19c7847bbe2bbf79a6fc40", "fileid": "a1cb2e7d607204223d1f32705cfadb70adc809d5db2433c73fc7560d3cf849da", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677790983" }, { "r": "4.7.0", "os": "win", "version": "1.15.0", "date": "2026-05-30T07:20:08.000Z", "commit": "74407d7cd88ef1665e19c7847bbe2bbf79a6fc40", "fileid": "b3f8e5cf444ebe7ff128dd82f7036bef22dca815b2feab6efa6fddc3278517f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677790983" }, { "r": "4.5.3", "os": "win", "version": "1.15.0", "date": "2026-05-30T07:21:23.000Z", "commit": "74407d7cd88ef1665e19c7847bbe2bbf79a6fc40", "fileid": "2c02c50e86bec6b5fdcee359bafec1b92cdae44c73f233f4ecfc25eff5512dce", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677790983" }, { "r": "4.6.0", "os": "win", "version": "1.15.0", "date": "2026-05-30T07:19:57.000Z", "commit": "74407d7cd88ef1665e19c7847bbe2bbf79a6fc40", "fileid": "85ecfc26138bd6f723ef79c63e44573c204124b0c04bbf4a1ff4fac75f1ec6a2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677790983" } ] }