{ "_id": "6abf5ac299f7aa8c6aa58c73", "Package": "mSigTools", "Type": "Package", "Title": "Mutational Signature Analysis Tools", "Version": "1.0.8", "Authors@R": "c(person(given = \"Steven\",\nfamily = \"Rozen\",\nrole = c(\"aut\", \"cre\"),\nemail = \"steverozen@pm.me\",\ncomment = c(ORCID = \"0000-0002-4288-0056\")),\nperson(given = \"Nanhai\",\nfamily = \"Jiang\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-4974-2753\")))", "Description": "Utility functions for mutational signature analysis as\ndescribed in Alexandrov, L. B. (2020)\n. This package provides two\ngroups of functions. One is for dealing with mutational\nsignature \"exposures\" (i.e. the counts of mutations in a sample\nthat are due to each mutational signature). The other group of\nfunctions is for matching or comparing sets of mutational\nsignatures. 'mSigTools' stands for mutational Signature\nanalysis Tools.", "License": "GPL-3", "URL": "https://github.com/Rozen-Lab/mSigTools", "BugReports": "https://github.com/Rozen-Lab/mSigTools/issues", "Encoding": "UTF-8", "Language": "en-US", "RoxygenNote": "7.2.3", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake", "Repository": "https://rozen-lab.r-universe.dev", "Date/Publication": "2024-04-13 08:02:46 UTC", "RemoteUrl": "https://github.com/rozen-lab/msigtools", "RemoteRef": "HEAD", "RemoteSha": "49ca85b0117e10a1ecd510998d54dc4426b29561", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-01 10:34:20 UTC", "User": "root" }, "Author": "Steven Rozen [aut, cre] (ORCID:\n),\nNanhai Jiang [aut] (ORCID: )", "Maintainer": "Steven Rozen ", "_user": "rozen-lab", "_type": "src", "_file": "mSigTools_1.0.8.tar.gz", "_fileid": "https://r2.ropensci.org/be6074c1918b6be72ed49b0a2b891c5f5bbfcb6106b34e287f65681552826db0", "_filesize": 152825, "_sha256": "be6074c1918b6be72ed49b0a2b891c5f5bbfcb6106b34e287f65681552826db0", "_expires": "2027-01-09T10:39:26.000Z", "_created": "2026-10-01T10:34:20.000Z", "_published": "2026-10-02T07:18:26.077Z", "_jobs": [ { "job": 110744720583, "time": 119, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11155460849" }, { "job": 110744720776, "time": 131, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11154349830" }, { "job": 110744720319, "time": 204, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11155415709" }, { "job": 110744718773, "time": 154, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11214295706" }, { "job": 110744719265, "time": 190, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11154629364" }, { "job": 110744720380, "time": 119, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11154913670" }, { "job": 110744720388, "time": 81, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11155510952" }, { "job": 110744721051, "time": 97, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11154179846" }, { "job": 110744720187, "time": 74, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11155530332" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/rozen-lab/actions/runs/36849623269", "_status": "success", "_upstream": "https://github.com/rozen-lab/msigtools", "_commit": { "id": "49ca85b0117e10a1ecd510998d54dc4426b29561", "author": "jnh01 <44010028+jnh01@users.noreply.github.com>", "committer": "jnh01 <44010028+jnh01@users.noreply.github.com>", "message": "Updated README\n", "time": 1712995366 }, "_maintainer": { "name": "Steven Rozen", "email": "steverozen@pm.me", "login": "steverozen", "description": "", "uuid": 30855154, "orcid": "0000-0002-4288-0056" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "clue", "role": "Imports" }, { "package": "philentropy", "role": "Imports" }, { "package": "quadprog", "role": "Imports" }, { "package": "sets", "role": "Imports" }, { "package": "cosmicsig", "role": "Suggests" }, { "package": "ICAMS", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "rozen-lab", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "jnh01", "count": 34, "uuid": 44010028 }, { "user": "steverozen", "count": 25, "uuid": 30855154 } ], "_userbio": { "uuid": 92154535, "type": "organization", "name": "Rozen-Lab", "followers": 3 }, "_downloads": { "count": 289, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mSigTools" }, "_devurl": "https://github.com/rozen-lab/msigtools", "_searchresults": 16, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/mSigTools.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/rozen-lab/msigtools", "_realowner": "rozen-lab", "_cranurl": true, "_releases": [ { "version": "1.0.5", "date": "2022-08-30" }, { "version": "1.0.7", "date": "2023-01-14" } ], "_exports": [ "find_best_reconstruction_QP", "match_two_sig_sets", "optimize_exposure_QP", "plot_exposure", "plot_exposure_to_pdf", "read_exposure", "sig_dist_matrix", "sort_exposure", "TP_FP_FN_avg_sim", "write_exposure" ], "_help": [ { "page": "find_best_reconstruction_QP", "title": "Find \"best\" reconstruction of a target signature or spectrum from a set of signatures.", "topics": [ "find_best_reconstruction_QP" ] }, { "page": "match_two_sig_sets", "title": "Find an optimal matching between two sets of signatures subject to a maximum distance.", "topics": [ "match_two_sig_sets" ] }, { "page": "optimize_exposure_QP", "title": "Quadratic programming optimization of signature activities", "topics": [ "optimize_exposure_QP" ] }, { "page": "plot_exposure", "title": "Plot exposures in multiple plots, with each plot showing exposures for a manageable number of samples.", "topics": [ "plot_exposure" ] }, { "page": "plot_exposure_to_pdf", "title": "Plot exposures in multiple plots to a single PDF file, with each plot showing exposures for a manageable number of samples.", "topics": [ "plot_exposure_to_pdf" ] }, { "page": "read_exposure", "title": "Read an exposure matrix from a file.", "topics": [ "read_exposure" ] }, { "page": "sig_dist_matrix", "title": "Compute a matrix of distances / similarities between two sets of signatures.", "topics": [ "sig_dist_matrix" ] }, { "page": "sort_exposure", "title": "Sort columns of an exposure matrix based on the number of mutations in each sample (column).", "topics": [ "sort_exposure" ] }, { "page": "TP_FP_FN_avg_sim", "title": "Find best matches (by cosine similarity) of a set of mutational signatures to a set of reference mutational signatures.", "topics": [ "TP_FP_FN_avg_sim" ] }, { "page": "write_exposure", "title": "Write an exposure matrix to a file.", "topics": [ "write_exposure" ] } ], "_readme": "https://github.com/rozen-lab/msigtools/raw/HEAD/README.md", "_rundeps": [ "clue", "cluster", "KernSmooth", "philentropy", "poorman", "quadprog", "Rcpp", "RcppParallel", "sets" ], "_score": 3.204119982655925, "_indexed": true, "_nocasepkg": "msigtools", "_universes": [ "rozen-lab", "steverozen" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.8", "date": "2026-10-01T10:36:23.000Z", "distro": "resolute", "commit": "49ca85b0117e10a1ecd510998d54dc4426b29561", "fileid": "https://r2.ropensci.org/ceb6da44f98869a5cdaf4e6a04e990a6d31d6f4620600e3d6c578b995d399034", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rozen-lab/actions/runs/36849623269" }, { "r": "4.6.1", "os": "linux", "version": "1.0.8", "date": "2026-10-01T10:38:41.000Z", "distro": "resolute", "commit": "49ca85b0117e10a1ecd510998d54dc4426b29561", "fileid": "https://r2.ropensci.org/add2374c066269d0e05bbb0a32e92b371dac9ea72bd7ec2c6110d87d4edff016", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rozen-lab/actions/runs/36849623269" }, { "r": "4.5.3", "os": "mac", "version": "1.0.8", "date": "2026-10-01T10:36:56.000Z", "commit": "49ca85b0117e10a1ecd510998d54dc4426b29561", "fileid": "https://r2.ropensci.org/025c84d3104d48c54d3d06f7986bfb55b4719194dc9ee852455744d749d6291f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rozen-lab/actions/runs/36849623269" }, { "r": "4.6.1", "os": "mac", "version": "1.0.8", "date": "2026-10-02T07:17:16.000Z", "commit": "49ca85b0117e10a1ecd510998d54dc4426b29561", "fileid": "https://r2.ropensci.org/3b91af4e1a36c1eae40caafcd16152222395bc7aacbe744aafa644cb4aaad32c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rozen-lab/actions/runs/36849623269" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.8", "date": "2026-10-01T10:36:33.000Z", "commit": "49ca85b0117e10a1ecd510998d54dc4426b29561", "fileid": "https://r2.ropensci.org/1518a94d97db1d119ac43dcb1a92ffa62703ef6e4664c810e56093a4e07b4192", "status": "success", "buildurl": "https://github.com/r-universe/rozen-lab/actions/runs/36849623269" }, { "r": "4.7.0", "os": "win", "version": "1.0.8", "date": "2026-10-01T10:35:37.000Z", "commit": "49ca85b0117e10a1ecd510998d54dc4426b29561", "fileid": "https://r2.ropensci.org/4773e6c588bab5d4a016f9ece9a012f52357ee26011e8e497d494469307c5a64", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rozen-lab/actions/runs/36849623269" }, { "r": "4.5.3", "os": "win", "version": "1.0.8", "date": "2026-10-01T10:35:53.000Z", "commit": "49ca85b0117e10a1ecd510998d54dc4426b29561", "fileid": "https://r2.ropensci.org/0ba72f482877d636387be6791ab1b4b892fc8f996806a8ff985af40a16e43e1f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rozen-lab/actions/runs/36849623269" }, { "r": "4.6.1", "os": "win", "version": "1.0.8", "date": "2026-10-01T10:35:31.000Z", "commit": "49ca85b0117e10a1ecd510998d54dc4426b29561", "fileid": "https://r2.ropensci.org/ee093b09bd2ef1503576be63d7b3f511d6449c415e6cd55a46dc46c6bd5d2053", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rozen-lab/actions/runs/36849623269" } ] }