{ "_id": "6a1addb21d7bb097a09eb2bc", "Package": "supersigs", "Title": "Supervised mutational signatures", "Version": "1.20.0", "Date": "2021-12-02", "Authors@R": "c(person(given = \"Albert\", \nfamily = \"Kuo\",\nrole = c(\"aut\", \"cre\"),\nemail = \"albertkuo@jhu.edu\",\ncomment = c(\"ORCID\" = \"0000-0001-5155-0748\")),\nperson(given = \"Yifan\",\nfamily = \"Zhang\",\nrole = c(\"aut\")),\nperson(given = \"Bahman\",\nfamily = \"Afsari\",\nrole = c(\"aut\")),\nperson(given = \"Cristian\",\nfamily = \"Tomasetti\",\nrole = c(\"aut\")))", "Description": "Generate SuperSigs (supervised mutational signatures) from\nsingle nucleotide variants in the cancer genome. Functions\nincluded in the package allow the user to learn supervised\nmutational signatures from their data and apply them to new\ndata. The methodology is based on the one described in Afsari\n(2021, ELife).", "biocViews": "FeatureExtraction, Classification, Regression, Sequencing,\nWholeGenome, SomaticMutation", "BugReports": "https://github.com/TomasettiLab/supersigs/issues", "URL": "https://tomasettilab.github.io/supersigs/", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "gzip", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "PackageStatus": "Deprecated", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:55:55 UTC", "RemoteUrl": "https://github.com/bioc/supersigs", "RemoteRef": "RELEASE_3_23", "RemoteSha": "589553e6b32b667080f7e3fb612c545d97dd971d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:12:39 UTC", "User": "root" }, "Author": "Albert Kuo [aut, cre] (ORCID: ),\nYifan Zhang [aut],\nBahman Afsari [aut],\nCristian Tomasetti [aut]", "Maintainer": "Albert Kuo ", "MD5sum": "7bcd0272fc147d00920d2d2c39d6c57b", "_user": "bioc-release", "_type": "src", "_file": "supersigs_1.20.0.tar.gz", "_fileid": "01434fdc38d9c735c79da910c3215a97acd9b419600380d5ae5de237efd1513f", "_filesize": 2797227, "_sha256": "01434fdc38d9c735c79da910c3215a97acd9b419600380d5ae5de237efd1513f", "_created": "2026-05-30T09:12:39.000Z", "_published": "2026-05-30T12:53:06.542Z", "_jobs": [ { "job": 78638915257, "time": 280, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307146597" }, { "job": 78638915281, "time": 453, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7307163012" }, { "job": 78638915288, "time": 488, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7307166054" }, { "job": 78638915312, "time": 228, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7308315472" }, { "job": 78638915283, "time": 241, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7308317980" }, { "job": 78638581850, "time": 399, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7307093624" }, { "job": 78638915274, "time": 232, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307142012" }, { "job": 78638915293, "time": 373, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7307154943" }, { "job": 78638915299, "time": 397, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7307157632" }, { "job": 78638915302, "time": 287, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7307147166" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679978877", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/supersigs", "_commit": { "id": "589553e6b32b667080f7e3fb612c545d97dd971d", "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": 1777380955 }, "_maintainer": { "name": "Albert Kuo", "email": "albertkuo@jhu.edu", "login": "pubg-prediction", "description": "", "uuid": 45675512, "orcid": "0000-0001-5155-0748" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "assertthat", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "rsample", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "VariantAnnotation", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_topics": [ "featureextraction", "classification", "regression", "sequencing", "wholegenome", "somaticmutation" ], "_stars": 3, "_contributors": [ { "user": "albertkuo", "count": 170, "uuid": 9829831 }, { "user": "nturaga", "count": 4, "uuid": 2746443 }, { "user": "yifanzhang17", "count": 4, "uuid": 16553037 } ], "_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/supersigs" }, "_devurl": "https://github.com/tomasettilab/supersigs", "_pkgdown": "https://tomasettilab.github.io/supersigs/", "_searchresults": 5, "_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/readme.html", "extra/readme.md", "extra/supersigs.html", "manual.pdf" ], "_cranurl": false, "_exports": [ "get_signature", "make_matrix", "partial_signature", "predict_signature", "process_vcf", "simplify_signature" ], "_datasets": [ { "name": "example_dt", "title": "Example dataset of mutations", "object": "example_dt", "class": [ "data.frame" ], "fields": [ "sample_id", "age", "chromosome", "position", "ref", "alt" ], "rows": 25, "table": true, "tojson": true }, { "name": "supersig_ls", "title": "Trained SuperSigs from TCGA", "object": "supersig_ls", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "example_dt", "title": "Example dataset of mutations", "topics": [ "example_dt" ] }, { "page": "get_signature", "title": "Function to obtain a SuperSig", "topics": [ "get_signature" ] }, { "page": "make_matrix", "title": "Function to transform mutations into \"matrix\" format", "topics": [ "make_matrix" ] }, { "page": "partial_signature", "title": "Function to remove the contribution of a SuperSig", "topics": [ "partial_signature" ] }, { "page": "predict_signature", "title": "Function to predict using SuperSig object", "topics": [ "predict_signature" ] }, { "page": "process_vcf", "title": "Function to transform VCF object into \"matrix\" format", "topics": [ "process_vcf" ] }, { "page": "simplify_signature", "title": "Function to simplify signature representation into interpretable labels for visualization purposes", "topics": [ "simplify_signature" ] }, { "page": "supersig_ls", "title": "Trained SuperSigs from TCGA", "topics": [ "supersig_ls" ] }, { "page": "SuperSig-class", "title": "An S4 class for SuperSig", "topics": [ "SuperSig", "SuperSig-class" ] } ], "_readme": "https://github.com/bioc/supersigs/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "assertthat", "Biobase", "BiocGenerics", "Biostrings", "caret", "class", "cli", "clock", "codetools", "cpp11", "crayon", "data.table", "DelayedArray", "diagram", "digest", "dplyr", "e1071", "farver", "foreach", "furrr", "future", "future.apply", "generics", "GenomicRanges", "ggplot2", "globals", "glue", "gower", "gtable", "hardhat", "ipred", "IRanges", "isoband", "iterators", "KernSmooth", "labeling", "lattice", "lava", "lifecycle", "listenv", "lubridate", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "ModelMetrics", "nlme", "nnet", "numDeriv", "parallelly", "pillar", "pkgconfig", "plyr", "pROC", "prodlim", "progressr", "proxy", "purrr", "R6", "RColorBrewer", "Rcpp", "recipes", "reshape2", "rlang", "rpart", "rsample", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "slider", "SparseArray", "sparsevctrs", "SQUAREM", "stringi", "stringr", "SummarizedExperiment", "survival", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tzdb", "utf8", "vctrs", "viridisLite", "warp", "withr", "XVector" ], "_score": 2.9542425094393248, "_indexed": false, "_nocasepkg": "supersigs", "_universes": [ "bioc-release" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-05-30T09:22:48.000Z", "distro": "noble", "commit": "589553e6b32b667080f7e3fb612c545d97dd971d", "fileid": "01451f59798396a681f71f049322f2aa646c3ac22e141381b13eac9c5e7c7f9e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679978877" }, { "r": "4.6.0", "os": "linux", "version": "1.20.0", "date": "2026-05-30T09:23:23.000Z", "distro": "noble", "commit": "589553e6b32b667080f7e3fb612c545d97dd971d", "fileid": "7d109cddaaa03b7e11a26900af4ae0f39e34006c6d833bbbad7e869beb42c0ed", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679978877" }, { "r": "4.5.3", "os": "mac", "version": "1.20.0", "date": "2026-05-30T12:50:35.000Z", "commit": "589553e6b32b667080f7e3fb612c545d97dd971d", "fileid": "46910a8a20331387900043200040b11fd0273336cbf127423e1a8df2a4a59300", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679978877" }, { "r": "4.6.0", "os": "mac", "version": "1.20.0", "date": "2026-05-30T12:51:03.000Z", "commit": "589553e6b32b667080f7e3fb612c545d97dd971d", "fileid": "fbe438af27547312f6738437e0954d5184df683acbf846f83ee2cedc42da0c94", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679978877" }, { "r": "4.6.0", "os": "wasm", "version": "1.20.0", "date": "2026-05-30T09:21:59.000Z", "commit": "589553e6b32b667080f7e3fb612c545d97dd971d", "fileid": "0d27c9de57d5b3aeceda17b89f0d0fbef014f1d25514b57290e1f41357cc25a9", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679978877" }, { "r": "4.7.0", "os": "win", "version": "1.20.0", "date": "2026-05-30T09:20:59.000Z", "commit": "589553e6b32b667080f7e3fb612c545d97dd971d", "fileid": "2fa7d4ba484be5f58e0e368e8a092af791900ffe568cd9619692382699d86a58", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679978877" }, { "r": "4.5.3", "os": "win", "version": "1.20.0", "date": "2026-05-30T09:21:43.000Z", "commit": "589553e6b32b667080f7e3fb612c545d97dd971d", "fileid": "4846031639a96c97ef8d75934833662840e0fa6a173a9c0e1d14e3496bf8d9d2", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679978877" }, { "r": "4.6.0", "os": "win", "version": "1.20.0", "date": "2026-05-30T09:20:44.000Z", "commit": "589553e6b32b667080f7e3fb612c545d97dd971d", "fileid": "0bf1b8a52579f79aee3e48451b1f3e32e9adea301e9c5da58adbc1d723c65b85", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679978877" } ] }