{ "_id": "6aca80f3fe5cc25786e8a68d", "Package": "MesKit", "Type": "Package", "Title": "A tool kit for dissecting cancer evolution from multi-region\nderived tumor biopsies via somatic alterations", "Version": "1.23.0", "Authors@R": "c(\nperson('Mengni', 'Liu', email = \"niinleslie@gmail.com\", role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-9938-9973')),\nperson('Jianyu', 'Chen', email = 'chenjy327@mail2.sysu.edu.cn', role = c('aut', 'ctb'), comment = c(ORCID = '0000-0003-4491-9265')),\nperson('Xin', 'Wang', email = 'wangx555@mail2.sysu.edu.cn', role = c('aut', 'ctb'), comment = c(ORCID = '0000-0002-6072-599X'))\n)", "Description": "MesKit provides commonly used analysis and visualization\nmodules based on mutational data generated by multi-region\nsequencing (MRS). This package allows to depict mutational\nprofiles, measure heterogeneity within or between tumors from\nthe same patient, track evolutionary dynamics, as well as\ncharacterize mutational patterns on different levels. Shiny\napplication was also developed for a need of GUI-based\nanalysis. As a handy tool, MesKit can facilitate the\ninterpretation of tumor heterogeneity and the understanding of\nevolutionary relationship between regions in MRS study.", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libglpk-dev libicu-dev libpng-dev libxml2-dev\nlibssl-dev perl zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:53:16 UTC", "RemoteUrl": "https://github.com/bioc/MesKit", "RemoteRef": "HEAD", "RemoteSha": "ee36e9486e29305e41e9f6a8b3499a3cbab88803", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 16:32:36 UTC", "User": "root" }, "Author": "Mengni Liu [aut, cre] (ORCID: ),\nJianyu Chen [aut, ctb] (ORCID: ),\nXin Wang [aut, ctb] (ORCID: )", "Maintainer": "Mengni Liu ", "_user": "bioc", "_type": "src", "_file": "MesKit_1.23.0.tar.gz", "_fileid": "https://r2.ropensci.org/3db709b9ff124df85da90a58c17635ebe5da01fd818ad2686532eae490f599e1", "_filesize": 3839191, "_sha256": "3db709b9ff124df85da90a58c17635ebe5da01fd818ad2686532eae490f599e1", "_expires": "2027-01-18T18:16:17.000Z", "_created": "2026-10-10T16:32:36.000Z", "_published": "2026-10-10T18:16:19.469Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38067653855", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 1, "warning": 1, "note": 15 }, "_upstream": "https://github.com/bioc/MesKit", "_commit": { "id": "ee36e9486e29305e41e9f6a8b3499a3cbab88803", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380796 }, "_maintainer": { "name": "Mengni Liu", "email": "niinleslie@gmail.com", "login": "niinleslie", "description": "", "uuid": 29459151, "orcid": "0000-0001-9938-9973" }, "_distro": "resolute", "_jobs": [ { "job": 114259856752, "time": 280, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11675677279" }, { "job": 114259856757, "time": 579, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11675772810" }, { "job": 114259856739, "time": 547, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11675996531" }, { "job": 114259856735, "time": 652, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11677988723" }, { "job": 114259856824, "time": 489, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11677749245" }, { "job": 114258539163, "time": 394, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11676380464" }, { "job": 114259856744, "time": 268, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11675358072" }, { "job": 114259856836, "time": 793, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11675703435" }, { "job": 114259856742, "time": 763, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11675778148" }, { "job": 114259856797, "time": 602, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11675348621" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.0.0", "role": "Imports" }, { "package": "ape", "version": ">= 5.4.1", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "pracma", "role": "Imports" }, { "package": "ggridges", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "circlize", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "mclust", "role": "Imports" }, { "package": "phangorn", "role": "Imports" }, { "package": "ComplexHeatmap", "version": ">= 1.9.3", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "shiny", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "version": ">= 1.4.0", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "clusterProfiler", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg19.knownGene", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23", "repository": "bioc" } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 539, "source": "https://www.bioconductor.org/packages/stats/bioc/MesKit" }, "_mentions": 1, "_searchresults": 20, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/MesKit.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "calFst", "calJSI", "calNeiDist", "ccfAUC", "classifyMut", "cna2gene", "compareCCF", "compareTree", "fitSignatures", "getBinaryMatrix", "getBootstrapValue", "getBranchType", "getCCFMatrix", "getMafData", "getMafPatient", "getMafRef", "getMutBranches", "getNonSyn_vc", "getPhyloTree", "getPhyloTreePatient", "getPhyloTreeRef", "getPhyloTreeTsbLabel", "getSampleInfo", "getTree", "getTreeMethod", "mathScore", "mutCluster", "mutHeatmap", "mutTrunkBranch", "plotCNA", "plotMutProfile", "plotMutSigProfile", "plotPhyloTree", "readMaf", "readSegment", "runMesKit", "subMaf", "testNeutral", "triMatrix" ], "_help": [ { "page": "calFst", "title": "calFst", "topics": [ "calFst" ] }, { "page": "calJSI", "title": "compareJSI", "topics": [ "calJSI" ] }, { "page": "calNeiDist", "title": "calNeiDist", "topics": [ "calNeiDist" ] }, { "page": "ccfAUC", "title": "ccfAUC", "topics": [ "ccfAUC" ] }, { "page": "classifyMut", "title": "classifyMut", "topics": [ "classifyMut" ] }, { "page": "cna2gene", "title": "cna2gene", "topics": [ "cna2gene" ] }, { "page": "compareCCF", "title": "compareCCF", "topics": [ "compareCCF" ] }, { "page": "compareTree", "title": "compareTree", "topics": [ "compareTree" ] }, { "page": "fitSignatures", "title": "fitSignatures", "topics": [ "fitSignatures" ] }, { "page": "getBinaryMatrix", "title": "getBinaryMatrix", "topics": [ "getBinaryMatrix", "getBinaryMatrix,phyloTree-method" ] }, { "page": "getBootstrapValue", "title": "getBootstrapValue", "topics": [ "getBootstrapValue", "getBootstrapValue,phyloTree-method" ] }, { "page": "getBranchType", "title": "getBranchType", "topics": [ "getBranchType", "getBranchType,phyloTree-method" ] }, { "page": "getCCFMatrix", "title": "getCCFMatrix", "topics": [ "getCCFMatrix", "getCCFMatrix,phyloTree-method" ] }, { "page": "getMafData", "title": "getMafData", "topics": [ "getMafData", "getMafData,Maf-method" ] }, { "page": "getMafPatient", "title": "getMafPatient", "topics": [ "getMafPatient", "getMafPatient,Maf-method" ] }, { "page": "getMafRef", "title": "getMafRef", "topics": [ "getMafRef", "getMafRef,Maf-method" ] }, { "page": "getMutBranches", "title": "getMutBranches", "topics": [ "getMutBranches", "getMutBranches,phyloTree-method" ] }, { "page": "getNonSyn_vc", "title": "getNonSyn_vc", "topics": [ "getNonSyn_vc", "getNonSyn_vc,Maf-method" ] }, { "page": "getPhyloTree", "title": "getPhyloTree", "topics": [ "getPhyloTree" ] }, { "page": "getPhyloTreePatient", "title": "getPhyloTreePatient", "topics": [ "getPhyloTreePatient", "getPhyloTreePatient,phyloTree-method" ] }, { "page": "getPhyloTreeRef", "title": "getPhyloTreeRef", "topics": [ "getPhyloTreeRef", "getPhyloTreeRef,phyloTree-method", "getPhyloTreeTsbLabel,phyloTree-method" ] }, { "page": "getPhyloTreeTsbLabel", "title": "getPhyloTreeRef", "topics": [ "getPhyloTreeTsbLabel" ] }, { "page": "getSampleInfo", "title": "getSampleInfo", "topics": [ "getSampleInfo", "getSampleInfo,Maf-method" ] }, { "page": "getTree", "title": "getTree", "topics": [ "getTree", "getTree,phyloTree-method" ] }, { "page": "getTreeMethod", "title": "getTreeMethod", "topics": [ "getTreeMethod", "getTreeMethod,phyloTree-method" ] }, { "page": "Maf-class", "title": "Maf class", "topics": [ "Maf", "Maf-class" ] }, { "page": "MafList-class", "title": "MafList class", "topics": [ "MafList", "MafList-class" ] }, { "page": "mathScore", "title": "mathScore", "topics": [ "mathScore" ] }, { "page": "mutCluster", "title": "mutCluster", "topics": [ "mutCluster" ] }, { "page": "mutHeatmap", "title": "mutHeatmap", "topics": [ "mutHeatmap" ] }, { "page": "mutTrunkBranch", "title": "mutTrunkBranch", "topics": [ "mutTrunkBranch" ] }, { "page": "phyloTree-class", "title": "phyloTree class", "topics": [ "phyloTree", "phyloTree-class" ] }, { "page": "phyloTreeList-class", "title": "phyloTreeList class", "topics": [ "phyloTreeList-class" ] }, { "page": "plotCNA", "title": "plotCNA", "topics": [ "plotCNA" ] }, { "page": "plotMutProfile", "title": "plotMutProfile", "topics": [ "plotMutProfile" ] }, { "page": "plotMutSigProfile", "title": "plotMutSigProfile", "topics": [ "plotMutSigProfile" ] }, { "page": "plotPhyloTree", "title": "plotPhyloTree", "topics": [ "plotPhyloTree" ] }, { "page": "readMaf", "title": "readMaf", "topics": [ "readMaf" ] }, { "page": "readSegment", "title": "readSegment", "topics": [ "readSegment" ] }, { "page": "runMesKit", "title": "Run the default MesKit app for analysis locally", "topics": [ "runMesKit" ] }, { "page": "subMaf", "title": "Subset Maf object", "topics": [ "subMaf" ] }, { "page": "testNeutral", "title": "testNeutral", "topics": [ "testNeutral" ] }, { "page": "triMatrix", "title": "triMatrix", "topics": [ "triMatrix" ] } ], "_readme": "https://github.com/bioc/MesKit/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "ape", "askpass", "Biobase", "BiocBaseUtils", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cowplot", "cpp11", "crayon", "curl", "data.table", "DBI", "digest", "doParallel", "dplyr", "farver", "fastmap", "fastmatch", "foreach", "generics", "GetoptLong", "ggplot2", "ggrepel", "ggridges", "GlobalOptions", "glue", "gtable", "httr", "igraph", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "matrixStats", "mclust", "memoise", "mime", "nlme", "openssl", "phangorn", "pillar", "pkgconfig", "png", "pracma", "purrr", "quadprog", "R6", "RColorBrewer", "Rcpp", "rjson", "rlang", "RSQLite", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "MesKit.Rmd", "filename": "MesKit.html", "title": "MesKit: Analyze and Visualize Multi-region Whole-exome Sequencing Data", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "1.1 Citation", "2. Prepare input Data", "2.1 MAF files", "2.2 Clinical data files", "2.3 CCF files", "2.4 Segmentation files", "3. Installation", "Via Bioconductor", "Via GitHub", "4. Start with the Maf object", "5. Mutational landscape", "5.1 Mutational profile", "5.2 CNA profile", "6. Measurement of intra-tumor heterogeneity", "6.1 Within tumors", "6.1.1 MATH score", "6.1.2 AUC of CCF", "6.1.3 Mutation clustering", "6.2 Between regions/tumors", "6.2.1 Fixation index", "6.2.2 Nei’s genetic distance", "7. Metastatic routes inference", "7.1 Pairwise CCF comparison", "7.2 Jaccard similarity index", "7.3 Neutral evolution", "8. Phylogenetic tree analysis", "8.1 Phylogenetic tree construction", "8.2 Compare Phylogenetic trees", "8.3 Functional exploration (custom module)", "8.4 Mutational characteristics analysis", "9. Phylogenetic tree visualization", "10. Shiny APP with video tutorial", "11. References", "12. Session Info" ], "created": "2019-12-02 12:54:44", "modified": "2021-05-07 02:07:02", "commits": 34 } ], "_score": 4.778151250383644, "_indexed": true, "_nocasepkg": "meskit", "_universes": [ "bioc", "niinleslie" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.0", "date": "2026-10-10T16:37:59.000Z", "distro": "resolute", "commit": "ee36e9486e29305e41e9f6a8b3499a3cbab88803", "fileid": "https://r2.ropensci.org/3b3d9520692efefe3f3695b7aeeba68f57664cfc8116111092cea1676ca6670e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067653855" }, { "r": "4.6.1", "os": "linux", "version": "1.23.0", "date": "2026-10-10T16:38:29.000Z", "distro": "resolute", "commit": "ee36e9486e29305e41e9f6a8b3499a3cbab88803", "fileid": "https://r2.ropensci.org/f230a15245192c302562fc1d3675e503db0821e1bf69f3cb8b7d70d246e3e613", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067653855" }, { "r": "4.5.3", "os": "mac", "version": "1.23.0", "date": "2026-10-10T18:08:30.000Z", "commit": "ee36e9486e29305e41e9f6a8b3499a3cbab88803", "fileid": "https://r2.ropensci.org/95e107bb44aaeb17c560da2ef3e1642513a5e75adb3df99d5f1c129260a0b7b9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067653855" }, { "r": "4.6.1", "os": "mac", "version": "1.23.0", "date": "2026-10-10T18:08:14.000Z", "commit": "ee36e9486e29305e41e9f6a8b3499a3cbab88803", "fileid": "https://r2.ropensci.org/e2829b531ceb479ae09a1343368613ead296ea98a659aa5b7432c8c41a9e09a3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067653855" }, { "r": "4.6.0", "os": "wasm", "version": "1.23.0", "date": "2026-10-10T16:37:34.000Z", "commit": "ee36e9486e29305e41e9f6a8b3499a3cbab88803", "fileid": "https://r2.ropensci.org/b2ff0b76e583e83a72f78d2bdf4f1b75e6a53f0576ca0f8b91b9eb9d74346ab8", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067653855" }, { "r": "4.7.0", "os": "win", "version": "1.23.0", "date": "2026-10-10T16:40:24.000Z", "commit": "ee36e9486e29305e41e9f6a8b3499a3cbab88803", "fileid": "https://r2.ropensci.org/8a8134faa888a0f39fae76407e450e027d859ef56f6742c7da57c09b6d89ce4c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067653855" }, { "r": "4.5.3", "os": "win", "version": "1.23.0", "date": "2026-10-10T16:40:29.000Z", "commit": "ee36e9486e29305e41e9f6a8b3499a3cbab88803", "fileid": "https://r2.ropensci.org/ab069aaced2c0286c2b670822d63c1a9293b54c74c07a83356aad6c8e93def8f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067653855" }, { "r": "4.6.1", "os": "win", "version": "1.23.0", "date": "2026-10-10T16:39:18.000Z", "commit": "ee36e9486e29305e41e9f6a8b3499a3cbab88803", "fileid": "https://r2.ropensci.org/0edce375ba3cc72cb154171be12430cad6f85c9c1e9179be35e699040bef72e3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067653855" } ] }