{ "_id": "6a27c8e024555f66ed540e5b", "Package": "CaMutQC", "Type": "Package", "Title": "An R Package for Comprehensive Filtration and Selection of\nCancer Somatic Mutations", "Version": "1.8.0", "Authors@R": "c(person(given = \"Xin\", family = \"Wang\", \nrole = c(\"aut\", \"cre\"),\nemail = \"sylviawang555@gmail.com\",\ncomment = c(ORCID = \"0000-0002-6072-599X\")))", "Description": "CaMutQC is able to filter false positive mutations\ngenerated due to technical issues, as well as to select\ncandidate cancer mutations through a series of well-structured\nfunctions by labeling mutations with various flags. And a\ndetailed and vivid filter report will be offered after\ncompleting a whole filtration or selection section. Also,\nCaMutQC integrates serveral methods and gene panels for Tumor\nMutational Burden (TMB) estimation.", "biocViews": "Software, QualityControl, GeneTarget", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "BugReports": "https://github.com/likelet/CaMutQC/issues", "URL": "https://github.com/likelet/CaMutQC", "License": "GPL-3", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl\nxz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:02:39 UTC", "RemoteUrl": "https://github.com/bioc/CaMutQC", "RemoteRef": "RELEASE_3_23", "RemoteSha": "fa2c753916d49075a7525a6b1619eb22f9858c9c", "Packaged": { "Date": "2026-06-09 06:25:08 UTC", "User": "root" }, "Author": "Xin Wang [aut, cre] (ORCID: )", "Maintainer": "Xin Wang ", "MD5sum": "81963e263a9a59d1708132206d4dc50f", "_user": "bioc-release", "_type": "src", "_file": "CaMutQC_1.8.0.tar.gz", "_fileid": "036ec62a3bc44ef8e942d6af3cf6d89f7bb8c92700bfd804e9f059852c979633", "_filesize": 5394102, "_sha256": "036ec62a3bc44ef8e942d6af3cf6d89f7bb8c92700bfd804e9f059852c979633", "_created": "2026-06-09T06:25:08.000Z", "_published": "2026-06-09T08:03:44.517Z", "_jobs": [ { "job": 80261421764, "time": 248, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7500112465" }, { "job": 80261421771, "time": 365, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7500144447" }, { "job": 80261421779, "time": 365, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7500144495" }, { "job": 80261421756, "time": 284, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7501857999" }, { "job": 80261421752, "time": 245, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7501834668" }, { "job": 80260612636, "time": 369, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7500044689" }, { "job": 80261421766, "time": 201, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7500099800" }, { "job": 80261421780, "time": 263, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7500116412" }, { "job": 80261421770, "time": 240, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7500110335" }, { "job": 80261421760, "time": 324, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7500132983" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187796601", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CaMutQC", "_commit": { "id": "fa2c753916d49075a7525a6b1619eb22f9858c9c", "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": 1777381359 }, "_maintainer": { "name": "Xin Wang", "email": "sylviawang555@gmail.com", "login": "wangxin555", "description": "", "uuid": 45935010, "orcid": "0000-0002-6072-599X" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "org.Hs.eg.db", "role": "Imports" }, { "package": "vcfR", "role": "Imports" }, { "package": "clusterProfiler", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "MesKit", "role": "Imports" }, { "package": "maftools", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-25", "n": 3 }, { "week": "2025-26", "n": 2 }, { "week": "2025-30", "n": 1 }, { "week": "2025-43", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.0", "bioc": "3.24" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23" } ], "_topics": [ "software", "qualitycontrol", "genetarget", "cancer-genomics", "somatic-mutations" ], "_stars": 8, "_contributors": [ { "user": "wangxin555", "count": 280, "uuid": 45935010 }, { "user": "likelet", "count": 5, "uuid": 3021506 }, { "user": "liujie1117", "count": 1, "uuid": 45936983 }, { "user": "shuhanzhao", "count": 1, "uuid": 70580527 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 224, "source": "https://www.bioconductor.org/packages/stats/bioc/CaMutQC" }, "_devurl": "https://github.com/likelet/camutqc", "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/CaMutQC.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/likelet/camutqc", "_realowner": "bioc", "_cranurl": false, "_exports": [ "calTMB", "mutFilterAdj", "mutFilterCan", "mutFilterCom", "mutFilterDB", "mutFilterNormalDP", "mutFilterPON", "mutFilterQual", "mutFilterRef", "mutFilterReg", "mutFilterSB", "mutFilterTech", "mutFilterType", "mutSelection", "processMut", "tomaftools", "toMesKit", "vcfToMAF" ], "_help": [ { "page": "calTMB", "title": "calTMB", "topics": [ "calTMB" ] }, { "page": "mutFilterAdj", "title": "mutFilterAdj", "topics": [ "mutFilterAdj" ] }, { "page": "mutFilterCan", "title": "mutFilterCan", "topics": [ "mutFilterCan" ] }, { "page": "mutFilterCom", "title": "mutFilterCom", "topics": [ "mutFilterCom" ] }, { "page": "mutFilterDB", "title": "mutFilterDB", "topics": [ "mutFilterDB" ] }, { "page": "mutFilterNormalDP", "title": "mutFilterNormalDP", "topics": [ "mutFilterNormalDP" ] }, { "page": "mutFilterPON", "title": "mutFilterPON", "topics": [ "mutFilterPON" ] }, { "page": "mutFilterQual", "title": "mutFilterQual", "topics": [ "mutFilterQual" ] }, { "page": "mutFilterRef", "title": "mutFilterRef", "topics": [ "mutFilterRef" ] }, { "page": "mutFilterReg", "title": "mutFilterReg", "topics": [ "mutFilterReg" ] }, { "page": "mutFilterSB", "title": "mutFilterSB", "topics": [ "mutFilterSB" ] }, { "page": "mutFilterTech", "title": "mutFilterTech", "topics": [ "mutFilterTech" ] }, { "page": "mutFilterType", "title": "mutFilterType", "topics": [ "mutFilterType" ] }, { "page": "mutSelection", "title": "mutSelection", "topics": [ "mutSelection" ] }, { "page": "processMut", "title": "processMut", "topics": [ "processMut" ] }, { "page": "tomaftools", "title": "tomaftools", "topics": [ "tomaftools" ] }, { "page": "toMesKit", "title": "toMeskit", "topics": [ "toMesKit" ] }, { "page": "vcfToMAF", "title": "vcfToMAF", "topics": [ "vcfToMAF" ] } ], "_readme": "https://github.com/bioc/CaMutQC/raw/RELEASE_3_23/README.md", "_rundeps": [ "aisdk", "AnnotationDbi", "ape", "aplot", "askpass", "base64enc", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "bslib", "cachem", "callr", "circlize", "cli", "clue", "cluster", "clusterProfiler", "codetools", "colorspace", "ComplexHeatmap", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "digest", "DNAcopy", "doParallel", "DOSE", "dplyr", "DT", "enrichit", "enrichplot", "evaluate", "farver", "fastmap", "fastmatch", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "foreach", "fs", "gdtools", "generics", "GetoptLong", "ggforce", "ggfun", "ggiraph", "ggnewscale", "ggplot2", "ggplotify", "ggrepel", "ggridges", "ggtangle", "ggtree", "GlobalOptions", "glue", "GO.db", "GOSemSim", "gridGraphics", "gson", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "httr2", "igraph", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "maftools", "magrittr", "MASS", "Matrix", "matrixStats", "mclust", "memoise", "memuse", "MesKit", "mgcv", "mime", "nlme", "openssl", "org.Hs.eg.db", "otel", "patchwork", "permute", "phangorn", "pheatmap", "pillar", "pinfsc50", "pkgconfig", "plyr", "png", "polyclip", "pracma", "processx", "promises", "ps", "purrr", "quadprog", "qvalue", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "Rhtslib", "rjson", "rlang", "rmarkdown", "RSQLite", "S4Vectors", "S7", "sass", "scales", "scatterpie", "Seqinfo", "shape", "stringi", "stringr", "survival", "sys", "systemfonts", "tibble", "tidydr", "tidyr", "tidyselect", "tidytree", "tinytex", "treeio", "tweenr", "utf8", "vcfR", "vctrs", "vegan", "viridisLite", "withr", "xfun", "XVector", "yaml", "yulab.utils" ], "_vignettes": [ { "source": "CaMutQC-manual.Rmd", "filename": "CaMutQC-manual.html", "title": "CaMutQC: Cancer Somatic Mutation Quality Control", "author": "Xin Wang sylviawang555@gmail.com", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Citation", "Installation", "Via Bioconductor (recommended)", "Via GitHub", "An Overview", "Input File", "Single VCF", "Multiple VCF", "From VCF to MAF", "Common filtering strategies", "Single filtration function", "Sequencing quality filtration", "Strand of Bias filtration", "Adjacent indel filtration", "Normal depth filtration", "Panel of Normals filtration", "Database filtration", "Variant type filtration", "Region selection", "Overall filtration", "Potential artifacts filtration", "Candidate variant selection", "Combined function: mutFilerCom", "Filter report", "TMB calculation", "Customized filtration", "Cancer type-based filtration", "Reference-based filtration", "Mutational analysis", "Union strategy", "Call strategy set by your name", "SessionInfo", "Reference" ], "created": "2021-11-15 02:44:44", "modified": "2025-10-20 05:33:40", "commits": 23 } ], "_score": 5.857332496431269, "_indexed": false, "_nocasepkg": "camutqc", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/CaMutQC", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.8.0", "date": "2026-06-09T06:29:14.000Z", "distro": "noble", "commit": "fa2c753916d49075a7525a6b1619eb22f9858c9c", "fileid": "8d5a9a8f6ee965d7dbecc4d925564703ac5ad2048b033e1b2c8a2f2564a21bac", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187796601" }, { "r": "4.6.0", "os": "linux", "version": "1.8.0", "date": "2026-06-09T06:29:17.000Z", "distro": "noble", "commit": "fa2c753916d49075a7525a6b1619eb22f9858c9c", "fileid": "d9b78ea3f7078d0cb931ac1be6165f9b47d582acc2ccd09f71f88e75021e1bd4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187796601" }, { "r": "4.5.3", "os": "mac", "version": "1.8.0", "date": "2026-06-09T08:00:46.000Z", "commit": "fa2c753916d49075a7525a6b1619eb22f9858c9c", "fileid": "625397516e639e0ce8bee2a12449d54f33881da54ead99bf477e3e4552d3ca92", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187796601" }, { "r": "4.6.0", "os": "mac", "version": "1.8.0", "date": "2026-06-09T07:59:55.000Z", "commit": "fa2c753916d49075a7525a6b1619eb22f9858c9c", "fileid": "f365660160bcdcad31d99b1a9c7c70a89f7493ea0d9fc5fb0cac696ad4f03a02", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187796601" }, { "r": "4.6.0", "os": "wasm", "version": "1.8.0", "date": "2026-06-09T06:29:07.000Z", "commit": "fa2c753916d49075a7525a6b1619eb22f9858c9c", "fileid": "e3807ed68b4c6773965c415a4ecceea3697f6661f3dba4896127c984e8cdad3d", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187796601" }, { "r": "4.7.0", "os": "win", "version": "1.8.0", "date": "2026-06-09T06:27:21.000Z", "commit": "fa2c753916d49075a7525a6b1619eb22f9858c9c", "fileid": "50c1bf571e37c5347c4302f6fbda4dc844d2f45a309195a485070ae245e343b2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187796601" }, { "r": "4.5.3", "os": "win", "version": "1.8.0", "date": "2026-06-09T06:27:23.000Z", "commit": "fa2c753916d49075a7525a6b1619eb22f9858c9c", "fileid": "fb2cb0f5d1bc3c7a19e9e7e32102e738d7ab75c442eadc7518dc61ca085c06e1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187796601" }, { "r": "4.6.0", "os": "win", "version": "1.8.0", "date": "2026-06-09T06:27:34.000Z", "commit": "fa2c753916d49075a7525a6b1619eb22f9858c9c", "fileid": "447d68337b287f81da3e2797c1dd95701a20d9a849318c840cd0797ee4b3cb09", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187796601" } ] }