{ "_id": "6a19712facfb0bcc41ded88d", "Package": "ACE", "Title": "Absolute Copy Number Estimation from Low-coverage Whole Genome\nSequencing", "Description": "Uses segmented copy number data to estimate tumor cell\npercentage and produce copy number plots displaying absolute\ncopy numbers.", "Version": "1.31.0", "Author": "Jos B Poell", "Maintainer": "Jos B Poell ", "biocViews": "CopyNumberVariation, DNASeq, Coverage, WholeGenome,\nVisualization, Sequencing", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "URL": "https://github.com/tgac-vumc/ACE", "RoxygenNote": "6.1.1", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 08:49:58 UTC", "User": "root" }, "Config/pak/sysreqs": "libbz2-dev liblzma-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:48:19 UTC", "RemoteUrl": "https://github.com/bioc/ACE", "RemoteRef": "HEAD", "RemoteSha": "96f7bbae689a1ceca90f1e3b9ba7e23a37ae49f5", "MD5sum": "5115a390bd1ef8d50e5691dce072b0a6", "_user": "bioc", "_type": "src", "_file": "ACE_1.31.0.tar.gz", "_fileid": "ba3090dc91dbca1b4846a44adc6fbaa3117006fda5b73289abc0db9c59ec8d53", "_filesize": 2596339, "_sha256": "ba3090dc91dbca1b4846a44adc6fbaa3117006fda5b73289abc0db9c59ec8d53", "_created": "2026-05-29T08:49:58.000Z", "_published": "2026-05-29T10:57:51.611Z", "_jobs": [ { "job": 78468816405, "time": 168, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7286866776" }, { "job": 78468816463, "time": 292, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7286906237" }, { "job": 78468816444, "time": 299, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7286908245" }, { "job": 78468816412, "time": 127, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7289040846" }, { "job": 78468816403, "time": 211, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7289064927" }, { "job": 78468171761, "time": 248, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7286815223" }, { "job": 78468816499, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7286856941" }, { "job": 78468816423, "time": 242, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7286891455" }, { "job": 78468816419, "time": 207, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7286878690" }, { "job": 78468816571, "time": 201, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7286877096" } ], "_bioccheck": { "error": 2, "warning": 1, "note": 19 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26627621750", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/ACE", "_commit": { "id": "96f7bbae689a1ceca90f1e3b9ba7e23a37ae49f5", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380499 }, "_maintainer": { "name": "Jos B Poell", "email": "j.poell@amsterdamumc.nl", "login": "jpoell", "description": "", "uuid": 25769357 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4", "role": "Depends" }, { "package": "Biobase", "role": "Imports" }, { "package": "QDNAseq", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-42", "n": 5 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23" } ], "_topics": [ "copynumbervariation", "dnaseq", "coverage", "wholegenome", "visualization", "sequencing" ], "_stars": 20, "_contributors": [ { "user": "jpoell", "count": 66, "uuid": 25769357 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "link-ny", "count": 1, "uuid": 4392950 }, { "user": "petanska", "count": 1, "uuid": 50733801 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 482, "source": "https://www.bioconductor.org/packages/stats/bioc/ACE" }, "_mentions": 478, "_devurl": "https://github.com/tgac-vumc/ace", "_searchresults": 42, "_rbuild": "4.6.0", "_assets": [ "extra/ACE.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/tgac-vumc/ace", "_realowner": "bioc", "_cranurl": false, "_exports": [ "ACEcall", "analyzegenomiclocations", "compresstemplate", "correlationmatrix", "correlationmatrixadjusted", "forcesegmentsontemplate", "getadjustedsegments", "linkvariants", "loopsquaremodel", "objectsampletotemplate", "ploidyplotloop", "postanalysisloop", "runACE", "segmentstotemplate", "singlemodel", "singleplot", "squaremodel", "squaremodelsummary", "templatefromequalsegments", "twosamplecompare" ], "_datasets": [ { "name": "copyNumbersSegmented", "title": "Segmented data of two tumor samples", "object": "copyNumbersSegmented", "class": [ "QDNAseqCopyNumbers" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "ACE-package", "title": "ACE package", "topics": [ "ACE-package", "ACE" ] }, { "page": "ACEcall", "title": "Categorize and plot subclonal, single, and double gains / losses", "topics": [ "ACEcall" ] }, { "page": "analyzegenomiclocations", "title": "Retrieve adjusted copy number information for specific genomic locations", "topics": [ "analyzegenomiclocations" ] }, { "page": "compresstemplate", "title": "Reduce the size of a template data frame", "topics": [ "compresstemplate" ] }, { "page": "copyNumbersSegmented", "title": "Segmented data of two tumor samples", "topics": [ "copyNumbersSegmented" ] }, { "page": "correlationmatrix", "title": "Create a correlation matrix of all samples in a QDNAseq-object", "topics": [ "correlationmatrix", "correlationmatrixadjusted" ] }, { "page": "forcesegmentsontemplate", "title": "Custom resegmentation with user-defined segment information", "topics": [ "forcesegmentsontemplate" ] }, { "page": "getadjustedsegments", "title": "Create a data frame with segment information corresponding to a model", "topics": [ "getadjustedsegments" ] }, { "page": "linkvariants", "title": "Append columns with total genomic copies and mutant copies to a file with variant/mutation data", "topics": [ "linkvariants" ] }, { "page": "loopsquaremodel", "title": "Create 'squaremodel' summaries for all samples in a QDNAseq-object", "topics": [ "loopsquaremodel" ] }, { "page": "objectsampletotemplate", "title": "Converts data of a sample in a QDNAseq-object to a template for ACE functions", "topics": [ "objectsampletotemplate" ] }, { "page": "postanalysisloop", "title": "Batch analysis of samples in a QDNAseq-object for which models have been chosen", "topics": [ "postanalysisloop" ] }, { "page": "runACE", "title": "Absolute Copy number Estimation", "topics": [ "ploidyplotloop", "runACE" ] }, { "page": "segmentstotemplate", "title": "Create a template data frame from input that only provides segment information", "topics": [ "segmentstotemplate" ] }, { "page": "singlemodel", "title": "Calculate potential fits for a single sample", "topics": [ "singlemodel" ] }, { "page": "singleplot", "title": "Plot an absolute copy number profile for a single sample", "topics": [ "singleplot" ] }, { "page": "squaremodel", "title": "Calculate potential fits for a single sample using ploidy as a variable", "topics": [ "squaremodel" ] }, { "page": "squaremodelsummary", "title": "Create a graphical summary of the result of squaremodel fitting", "topics": [ "squaremodelsummary" ] }, { "page": "templatefromequalsegments", "title": "Create a template data frame with artificial segments of equal length", "topics": [ "templatefromequalsegments" ] }, { "page": "twosamplecompare", "title": "Overlay copy number data of two samples and compare segment values", "topics": [ "twosamplecompare" ] } ], "_readme": "https://github.com/bioc/ACE/raw/HEAD/README.md", "_rundeps": [ "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bitops", "CGHbase", "CGHcall", "cli", "codetools", "cpp11", "crayon", "digest", "DNAcopy", "farver", "formatR", "futile.logger", "futile.options", "future", "future.apply", "generics", "GenomicRanges", "ggplot2", "globals", "glue", "gtable", "impute", "IRanges", "isoband", "labeling", "lambda.r", "lifecycle", "limma", "listenv", "marray", "matrixStats", "parallelly", "QDNAseq", "R.methodsS3", "R.oo", "R.utils", "R6", "RColorBrewer", "Rhtslib", "rlang", "Rsamtools", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "snowfall", "statmod", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "ACE_vignette.Rmd", "filename": "ACE_vignette.html", "title": "ACE vignette", "author": "Jos B. Poell", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Why use ACE?", "How ACE works", "Running ACE", "Installation", "Getting started", "ACE output", "rds-file", "rds subdirectories", "ploidies subdirectories", "summaries", "likelyfits subdirectory", "individual sample subdirectories", "fitpicker tables", "Model selection", "Examining single samples", "Advanced functions", "getadjustedsegments", "linkvariants", "analyzegenomiclocations", "postanalysisloop", "Advanced use", "Considerations for larger data sets", "Error methods", "Penalizing lower cellularities", "Chromosomal subsets", "Sex chromosomes", "Additional Functionality (accessory functions)", "ACEcall", "twosamplecompare", "squaremodelsummary", "loopsquaremodel", "Information", "Contact", "License", "Reference", "Session information" ], "created": "2018-05-22 13:30:12", "modified": "2021-01-15 16:16:34", "commits": 9 } ], "_score": 7.799340549453581, "_indexed": true, "_nocasepkg": "ace", "_universes": [ "bioc", "jpoell", "tgac-vumc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-05-29T08:53:31.000Z", "distro": "noble", "commit": "96f7bbae689a1ceca90f1e3b9ba7e23a37ae49f5", "fileid": "1d02921d702e93a8e86842e0b1fc97373c08668a447c776482d17a74d5a950bf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627621750" }, { "r": "4.6.0", "os": "linux", "version": "1.31.0", "date": "2026-05-29T08:53:33.000Z", "distro": "noble", "commit": "96f7bbae689a1ceca90f1e3b9ba7e23a37ae49f5", "fileid": "db633d8c313789c28b6567712714818ad7d3fe0c557ef95cdad90f8a2e883808", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627621750" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", "date": "2026-05-29T10:55:00.000Z", "commit": "96f7bbae689a1ceca90f1e3b9ba7e23a37ae49f5", "fileid": "2ed18520c1489892d3198ab13d24e7381b12cd2889d403fbc05eac12963b77d8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627621750" }, { "r": "4.6.0", "os": "mac", "version": "1.31.0", "date": "2026-05-29T10:55:48.000Z", "commit": "96f7bbae689a1ceca90f1e3b9ba7e23a37ae49f5", "fileid": "1b41587f031b7aae30c80bf955fd95c5e0eba93f9f11f3a6b53258e7351de25e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627621750" }, { "r": "4.6.0", "os": "wasm", "version": "1.31.0", "date": "2026-05-29T08:52:45.000Z", "commit": "96f7bbae689a1ceca90f1e3b9ba7e23a37ae49f5", "fileid": "310b8db2b4f0b342923c61efbbcc77ec996b5fe339510f8f0c4237be7ee1e7f3", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627621750" }, { "r": "4.7.0", "os": "win", "version": "1.31.0", "date": "2026-05-29T08:52:30.000Z", "commit": "96f7bbae689a1ceca90f1e3b9ba7e23a37ae49f5", "fileid": "4f1ceffa97044d3398c25190b56853d2bbf02181a5dfafeb971de57932879d6a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627621750" }, { "r": "4.5.3", "os": "win", "version": "1.31.0", "date": "2026-05-29T08:51:47.000Z", "commit": "96f7bbae689a1ceca90f1e3b9ba7e23a37ae49f5", "fileid": "8cd1c867200aa8bd00924eb86b42461c658520809ea1489904e16700303d2427", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627621750" }, { "r": "4.6.0", "os": "win", "version": "1.31.0", "date": "2026-05-29T08:51:48.000Z", "commit": "96f7bbae689a1ceca90f1e3b9ba7e23a37ae49f5", "fileid": "29f6e06311d16199444673b9cdb6eb0de0e4021aec3156ce58d164b2b96c7b86", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627621750" } ] }