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Bootstrapping is performed as part of the analysis.\nThe framework supports parallelization and is optimized for use\non multi-core systems. The software was described by Fantini D\net al (2020) and is based on a\ncustom R-based implementation of the original MATLAB WTSI\nframework by Alexandrov LB et al (2013)\n.", "License": "GPL-2", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "LazyData": "true", "URL": "https://www.data-pulse.com/dev_site/mutsignatures/", "RoxygenNote": "7.2.1", "Repository": "https://dami82.r-universe.dev", "Date/Publication": "2023-01-18 21:22:55 UTC", "RemoteUrl": "https://github.com/dami82/mutsignatures", "RemoteRef": "HEAD", "RemoteSha": "ad406018266f80a3048ae6219bf6c09cf6f69134", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 06:47:24 UTC", "User": "root" }, "MD5sum": "dcb6393e55521720f50b4826cf94af70", "_user": "dami82", "_type": "src", "_file": "mutSignatures_2.1.5.tar.gz", "_fileid": "9858f7c37badc62c24f232d06d4333c9f91d160856d62956fe186563e3a0fb6f", "_filesize": 972407, "_sha256": "9858f7c37badc62c24f232d06d4333c9f91d160856d62956fe186563e3a0fb6f", "_created": "2026-05-31T06:47:24.000Z", "_published": "2026-05-31T07:33:35.992Z", "_distro": "noble", "_jobs": [ { "job": 78706570208, "time": 150, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7314562444" }, { "job": 78706570212, "time": 147, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7314562089" }, { "job": 78706570194, "time": 126, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7314841599" }, { "job": 78706570207, "time": 105, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7314848679" }, { "job": 78706391523, "time": 210, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7314546768" }, { "job": 78706570193, "time": 105, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7314557923" }, { "job": 78706570203, "time": 116, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7314558845" }, { "job": 78706570200, "time": 102, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7314557433" }, { "job": 78706570202, "time": 100, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7314557361" } ], "_buildurl": "https://github.com/r-universe/dami82/actions/runs/26705667490", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/dami82/mutsignatures", "_commit": { "id": "ad406018266f80a3048ae6219bf6c09cf6f69134", "author": "dami82 ", "committer": "dami82 ", "message": "Replacing mutSigData.rda file. 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"mutSignatures-package" ] }, { "page": "sub-mutationCounts-numeric-ANY-ANY-method", "title": "Subset a mutationCounts-class object.", "topics": [ "[,mutationCounts,numeric,ANY,ANY-method", "[,mutationCounts,numeric-method" ] }, { "page": "sub-mutationSignatures-numeric-ANY-ANY-method", "title": "Subset a mutationSignatures-class object.", "topics": [ "[,mutationSignatures,numeric,ANY,ANY-method", "[,mutationSignatures,numeric-method" ] }, { "page": "sub-mutSignExposures-numeric-ANY-ANY-method", "title": "Subset a mutSignExposures-class object.", "topics": [ "[,mutSignExposures,numeric,ANY,ANY-method", "[,mutSignExposures,numeric-method" ] }, { "page": "as.data.frame-mutationCounts-method", "title": "Convert a mutationCounts object to data.frame.", "topics": [ "as.data.frame,mutationCounts-method" ] }, { "page": "as.data.frame-mutationSignatures-method", "title": "Convert a mutationSignatures object to data.frame.", "topics": [ "as.data.frame,mutationSignatures-method" ] }, { "page": "as.data.frame-mutSignExposures-method", "title": "Convert and/or transpose a mutSignExposures object to data.frame.", "topics": [ "as.data.frame,mutSignExposures-method" ] }, { "page": "as.list-mutationSignatures-method", "title": "Convert a mutationSignatures object to list.", "topics": [ "as.list,mutationSignatures-method" ] }, { "page": "as.list-mutFrameworkParams-method", "title": "Convert a mutFrameworkParams object to list.", "topics": [ "as.list,mutFrameworkParams-method" ] }, { "page": "as.matrix-mutationCounts-method", "title": "Convert a mutationCounts object to matrix.", "topics": [ "as.matrix,mutationCounts-method" ] }, { "page": "as.mutation.counts", "title": "Method as.mutation.counts.", "topics": [ "as.mutation.counts", "as.mutation.counts,data.frame,ANY,ANY-method", "as.mutation.counts,data.frame-method" ] }, { "page": "as.mutation.signatures", "title": "Method as.mutation.signatures.", "topics": [ "as.mutation.signatures", "as.mutation.signatures,data.frame-method" ] }, { "page": "as.mutsign.exposures", "title": "Method as.mutsign.exposures.", "topics": [ "as.mutsign.exposures", "as.mutsign.exposures,data.frame,logical-method" ] }, { "page": "attachContext", "title": "Attach Nucleotide Context.", "topics": [ "attachContext" ] }, { "page": "attachMutType", "title": "Attach Mutation Types.", "topics": [ "attachMutType" ] }, { "page": "cbind2", "title": "Combine two mutationSignatures-class objects.", "topics": [ "cbind2", "cbind2,mutationSignatures,mutationSignatures-method" ] }, { "page": "coerceObj-methods", "title": "Method coerceObj.", "topics": [ "coerceObj", "coerceObj,data.frame,character-method", "coerceObj,mutationCounts,character-method", "coerceObj,mutationSignatures,character-method", "coerceObj,mutFrameworkParams,character-method", "coerceObj,mutSignExposures,character-method" ] }, { "page": "countMutTypes", "title": "Count Mutation Types.", "topics": [ "countMutTypes" ] }, { "page": "decipherMutationalProcesses", "title": "Decipher Mutational Processes Contributing to a Collection of Genomic Mutations.", "topics": [ "decipherMutationalProcesses" ] }, { "page": "extractXvarlinkData", "title": "Extract Variants from XvarlinkData.", "topics": [ "extractXvarlinkData" ] }, { "page": "filterSNV", "title": "Filter Single Nucleotide Variants.", "topics": [ "filterSNV" ] }, { "page": "frequencize", "title": "Convert Mutation COunts to PerMille Frequencies.", "topics": [ "frequencize" ] }, { "page": "getCosmicSignatures", "title": "Obtain COSMIC mutational Signatures.", "topics": [ "getCosmicSignatures" ] }, { "page": "getCounts", "title": "Method getCounts.", "topics": [ "getCounts", "getCounts,mutationCounts-method" ] }, { "page": "getFwkParam", "title": "Method getFwkParam.", "topics": [ "getFwkParam", "getFwkParam,mutFrameworkParams,character-method" ] }, { "page": "getMutationTypes", "title": "Method getMutationTypes.", "topics": [ "getMutationTypes", "getMutationTypes,mutationCounts-method", "getMutationTypes,mutationSignatures-method" ] }, { "page": "getSampleIdentifiers", "title": "Method getSampleIdentifiers.", "topics": [ "getSampleIdentifiers", "getSampleIdentifiers,mutationCounts-method", "getSampleIdentifiers,mutSignExposures-method" ] }, { "page": "getSignatureIdentifiers", "title": "Method getSignatureIdentifiers.", "topics": [ "getSignatureIdentifiers", "getSignatureIdentifiers,mutationSignatures-method", "getSignatureIdentifiers,mutSignExposures-method" ] }, { "page": "importVCFfiles", "title": "Import Mutation data from VCF files.", "topics": [ "importVCFfiles" ] }, { "page": "matchSignatures", "title": "Match Mutational Signatures.", "topics": [ "matchSignatures" ] }, { "page": "msigPlot", "title": "Method msigPlot.", "topics": [ "msigPlot", "msigPlot,mutationCounts-method", "msigPlot,mutationSignatures-method", "msigPlot,mutSignExposures-method" ] }, { "page": "mutationCounts-class", "title": "Class mutationCounts.", "topics": [ "initialize,mutationCounts-method", "mutationCounts-class" ] }, { "page": "mutationSignatures-class", "title": "Class mutationSignatures.", "topics": [ "initialize,mutationSignatures-method", "mutationSignatures-class" ] }, { "page": "mutFrameworkParams-class", "title": "Class mutFrameworkParams.", "topics": [ "initialize,mutFrameworkParams-method", "mutFrameworkParams-class" ] }, { "page": "mutSigData", "title": "Input Data and Examples for Running Mutational Signatures Analyses", "topics": [ "mutSigData" ] }, { "page": "mutSignExposures-class", "title": "Class mutSignExposures.", "topics": [ "initialize,mutSignExposures-method", "mutSignExposures-class" ] }, { "page": "plotMutTypeProfile", "title": "Plot Mutation Signature Profiles.", "topics": [ "plotMutTypeProfile" ] }, { "page": "plotSignExposures", "title": "Plot Signature Exposure Profiles.", "topics": [ "plotSignExposures" ] }, { "page": "prelimProcessAssess", "title": "Run a Preliminary Process Assess analysis.", "topics": [ "prelimProcessAssess" ] }, { "page": "processVCFdata", "title": "Process VCF data.", "topics": [ "processVCFdata" ] }, { "page": "removeMismatchMut", "title": "Remove Mismatched Mutations.", "topics": [ "removeMismatchMut" ] }, { "page": "resolveMutSignatures", "title": "Resolve Mutation Signatures.", "topics": [ "resolveMutSignatures" ] }, { "page": "revCompl", "title": "Compute Reverse Complement sequences.", "topics": [ "revCompl" ] }, { "page": "setFwkParam", "title": "Method setFwkParam.", "topics": [ "setFwkParam", "setFwkParam,mutFrameworkParams,character,ANY-method", "setFwkParam,mutFrameworkParams,character-method" ] }, { "page": "setMutClusterParams", "title": "Set Parameters for Extracting Mutational Signatures.", "topics": [ "setMutClusterParams" ] }, { "page": "setSignatureNames", "title": "Method setSignatureNames.", "topics": [ "setSignatureNames", "setSignatureNames,mutationSignatures,character-method" ] }, { "page": "mutationCounts-show", "title": "Show method of the mutationCounts Class.", "topics": [ "print,mutationCounts-method", "show,mutationCounts-method" ] }, { "page": "mutationSignatures-show", "title": "Show method of the mutationSignatures Class.", "topics": [ "print,mutationSignatures-method", "show,mutationSignatures-method" ] }, { "page": "mutFrameworkParams-show", "title": "Show method of the mutFrameworkParams Class.", "topics": [ "print,mutFrameworkParams-method", "show,mutFrameworkParams-method" ] }, { "page": "mutSignExposures-show", "title": "Show method of the mutSignExposures Class.", "topics": [ "print,mutSignExposures-method", "show,mutSignExposures-method" ] }, { "page": "silhouetteMLB", "title": "Silhouette Analysis.", "topics": [ "silhouetteMLB" ] }, { "page": "simplifySignatures", "title": "Simplify Mutational Signatures.", "topics": [ "simplifySignatures" ] }, { "page": "sortByMutations", "title": "Sort Data by Mutation Type.", "topics": [ "sortByMutations" ] }, { "page": "table2df", "title": "Table Mutation Types by Sample.", "topics": [ "table2df" ] } ], "_readme": "https://github.com/dami82/mutsignatures/raw/HEAD/README.md", "_rundeps": [ "cli", "cluster", "codetools", "cpp11", "doParallel", "farver", "foreach", "ggplot2", "glue", "gtable", "isoband", "iterators", "labeling", "lifecycle", "pracma", "proxy", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "get_sarted_with_mutSignatures.Rmd", "filename": "get_sarted_with_mutSignatures.html", "title": "Getting Started with mutSignatures", "author": "Damiano Fantini, Ph.D.", "engine": "knitr::rmarkdown", "headings": [ "Tutorials and How-tos", "Installation", "Note on software Dependencies", "Pipeline", "Alternative pipeline", "Load library, set-up environment", "Example 1 - De novo extraction of Mutational Signatures from BLCA samples", "Data Import and pre-processing", "Signature Extraction", "Downstream analyses and visualization", "Example 2 - Estimate the contribution of a panel of known mutational signatures", "Estimate Exposures to known Mutational Signatures", "Downstream analysis", "More info and examples", "SessionInfo" ], "created": "2022-08-23 02:25:17", "modified": "2022-08-25 15:22:53", "commits": 3 } ], "_score": 5.90200289135073, "_indexed": true, "_nocasepkg": "mutsignatures", "_universes": [ "dami82" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.1.5", "date": "2026-05-31T06:49:41.000Z", "distro": "noble", "commit": "ad406018266f80a3048ae6219bf6c09cf6f69134", "fileid": "463b42329061a5603da639ebd7a4f22edfa2d5325ab5da5745bb5d5af94320c5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dami82/actions/runs/26705667490" }, { "r": "4.6.0", "os": "linux", "version": "2.1.5", "date": "2026-05-31T06:49:39.000Z", "distro": "noble", "commit": "ad406018266f80a3048ae6219bf6c09cf6f69134", "fileid": "ab557fb9cf13d768c7ce66af19208f159a92711fda4a3fe232025a94995716ca", "status": "success", "check": "OK", "buildurl": 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