{ "_id": "6a4942fe18cdde069385e92e", "Package": "methInheritSim", "Type": "Package", "Title": "Simulating Whole-Genome Inherited Bisulphite Sequencing Data", "Description": "Simulate a multigeneration methylation case versus control\nexperiment with inheritance relation using a real control\ndataset.", "Version": "1.35.0", "Date": "2025-07-22", "Author": "Pascal Belleau, Astrid Deschênes and Arnaud Droit", "Author@R": "c(person(\"Pascal\", \"Belleau\",\nemail=\"pascal_belleau@hotmail.com\", role=c(\"cre\", \"aut\")),\nperson(\"Astrid\", \"Deschênes\", email=\"adeschen@hotmail.com\",\nrole=c(\"aut\")), person(\"Arnaud\", \"Droit\",\nemail=\"arnaud.droit@crchuq.ulaval.ca\", role=c(\"aut\")))", "Encoding": "UTF-8", "License": "Artistic-2.0", "URL": "https://github.com/belleau/methInheritSim", "BugReports": "https://github.com/belleau/methInheritSim/issues", "VignetteBuilder": "knitr", "biocViews": "BiologicalQuestion, Epigenetics, DNAMethylation,\nDifferentialMethylation, MethylSeq, Software, ImmunoOncology,\nStatisticalMethod, WholeGenome, Sequencing", "Maintainer": "Pascal Belleau ", "RoxygenNote": "6.0.1", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:45:44 UTC", "RemoteUrl": "https://github.com/bioc/methInheritSim", "RemoteRef": "HEAD", "RemoteSha": "17b462cd6d1e551cda340dc26e890ce88e86a313", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 11:26:23 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "methInheritSim_1.35.0.tar.gz", "_fileid": "https://r2.ropensci.org/40261c44407f29c65f1a3d8a3f8e8e532de20732c66eac8180ff55695f5bd7ed", "_filesize": 1074265, "_sha256": "40261c44407f29c65f1a3d8a3f8e8e532de20732c66eac8180ff55695f5bd7ed", "_expires": "2026-10-12T17:29:32.000Z", "_created": "2026-07-04T11:26:23.000Z", "_published": "2026-07-04T17:29:34.808Z", "_bioccheck": { "error": 1, "warning": 1, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28704586639", "_status": "success", "_upstream": "https://github.com/bioc/methInheritSim", "_commit": { "id": "17b462cd6d1e551cda340dc26e890ce88e86a313", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380344 }, "_maintainer": { "name": "Pascal Belleau", "email": "pascal_belleau@hotmail.com", "login": "belleau", "description": "Computational Postdoctoral Fellow", "uuid": 8398253 }, "_distro": "resolute", "_jobs": [ { "job": 85152305950, "time": 211, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8081283723" }, { "job": 85152305884, "time": 413, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8081307376" }, { "job": 85152305976, "time": 463, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8081313561" }, { "job": 85152305999, "time": 195, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8081289829" }, { "job": 85152305979, "time": 252, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8081291191" }, { "job": 85152305777, "time": 352, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8081260647" }, { "job": 85152305930, "time": 194, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8081281815" }, { "job": 85152306006, "time": 330, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8081297972" }, { "job": 85152306097, "time": 331, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8081298129" }, { "job": 85152306088, "time": 311, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8081295788" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "methylKit", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "msm", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "methylInheritance", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.35.0", "bioc": "3.24" }, { "branch": "release", "version": "1.34.0", "bioc": "3.23" } ], "_topics": [ "biologicalquestion", "epigenetics", "dnamethylation", "differentialmethylation", "methylseq", "software", "immunooncology", "statisticalmethod", "wholegenome", "sequencing", "bisulphite-sequencing", "inheritance", "methylation", "simulation" ], "_stars": 2, "_contributors": [ { "user": "adeschen", "count": 230, "uuid": 7254636 }, { "user": "belleau", "count": 122, "uuid": 8398253 }, { "user": "nturaga", "count": 4, "uuid": 2746443 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/belleau/methinheritsim", "_searchresults": 2, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/methInheritSim.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/belleau/methinheritsim", "_realowner": "bioc", "_cranurl": false, "_exports": [ "runSim" ], "_datasets": [ { "name": "dataSimExample", "title": "A 'list' containing methylation information used by some internal functions (for demo purpose.", "object": "dataSimExample", "file": "dataSimExample.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "samplesForChrSynthetic", "title": "All samples information, formated by 'methylKit', in a 'methylBase' format (for demo purpose).", "object": "samplesForChrSynthetic", "file": "samplesForChrSynthetic.RData", "class": [ "methylBase" ], "fields": [ "chr", "start", "end", "strand", "coverage1", "numCs1", "numTs1", "coverage2", "numCs2", "numTs2", "coverage3", "numCs3", "numTs3", "coverage4", "numCs4", "numTs4", "coverage5", "numCs5", "numTs5", "coverage6", "numCs6", "numTs6", "coverage7", "numCs7", "numTs7", "coverage8", "numCs8", "numTs8", "coverage9", "numCs9", "numTs9", "coverage10", "numCs10", "numTs10", "coverage11", "numCs11", "numTs11", "coverage12", "numCs12", "numTs12" ], "rows": 9864, "table": true, "tojson": true } ], "_help": [ { "page": "methInheritSim-package", "title": "methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data", "topics": [ "methInheritSim-package", "methInheritSim" ] }, { "page": "dataSimExample", "title": "A 'list' containing methylation information used by some internal functions (for demo purpose.", "topics": [ "dataSimExample" ] }, { "page": "runSim", "title": "Simulate a multigeneration methylation experiment with inheritance", "topics": [ "runSim" ] }, { "page": "samplesForChrSynthetic", "title": "All samples information, formated by 'methylKit', in a 'methylBase' format (for demo purpose).", "topics": [ "samplesForChrSynthetic" ] } ], "_readme": "https://github.com/bioc/methInheritSim/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "bbmle", "bdsmatrix", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "cigarillo", "cli", "coda", "codetools", "cpp11", "crayon", "curl", "data.table", "DelayedArray", "emdbook", "expm", "farver", "fastseg", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "glue", "gtable", "gtools", "httr", "IRanges", "isoband", "jsonlite", "KernSmooth", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "methylKit", "mgcv", "mime", "msm", "mvtnorm", "nlme", "numDeriv", "openssl", "pillar", "pkgconfig", "plyr", "qvalue", "R.methodsS3", "R.oo", "R.utils", "R6", "RColorBrewer", "Rcpp", "RCurl", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "utf8", "vctrs", "viridisLite", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "methInheritSim.Rmd", "filename": "methInheritSim.html", "title": "Simulating Whole-Genome Inherited Bisulphite Sequencing Data", "author": "Pascal Belleau, Astrid Deschênes and Arnaud Droit", "engine": "knitr::rmarkdown", "headings": [ "Licensing", "Citing", "Introduction", "Loading methInheritSim package", "Description of the simulation process", "Simulated control dataset", "Simulated case dataset", "Case study", "The simulated dataset", "The simulation", "Files generated by the simulation", "Synthetic chromosome in GRanges format (\"syntheticChr\" prefix)", "Simulation information in GRanges format (\"simData\" prefix)", "Information about DMS state (\"stateDiff\" prefix)", "Files related to saveGRanges parameter", "Raw methylation data for all samples in GRanges format (\"methylGR\" prefix)", "Information about controls and cases (\"treatment\" prefix)", "Files related to saveMethylKit parameter", "Raw methylation data in methylRaw format (\"methylObj\" prefix)", "Files related to runAnalysis parameter", "Methylation events present in multiple samples in methylBase format (\"meth\" prefix)", "Differential methylation statistics in methylDiff format (\"methDiff\" prefix)", "Conclusion" ], "created": "2017-03-30 12:29:38", "modified": "2018-09-29 21:16:52", "commits": 5 } ], "_score": 5.079181246047625, "_indexed": true, "_nocasepkg": "methinheritsim", "_universes": [ "bioc", "belleau" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-07-04T11:30:10.000Z", "distro": "resolute", "commit": "17b462cd6d1e551cda340dc26e890ce88e86a313", "fileid": "https://r2.ropensci.org/7be174f85e230b95a942da80fcb217310948bbe0ec21ff465586ce3e31842076", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704586639" }, { "r": "4.6.1", "os": "linux", "version": "1.35.0", "date": "2026-07-04T11:31:06.000Z", "distro": "resolute", "commit": "17b462cd6d1e551cda340dc26e890ce88e86a313", "fileid": "https://r2.ropensci.org/72c672fba9a74e78e7b18da02fd49871486d569a731060f93aefa54f625145c8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704586639" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-07-04T11:29:29.000Z", "commit": "17b462cd6d1e551cda340dc26e890ce88e86a313", "fileid": "https://r2.ropensci.org/3db13e01713ca4820a8e8fbe43aa4d8541b8bef2c79a56f57336fadcb3f3d875", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704586639" }, { "r": "4.6.1", "os": "mac", "version": "1.35.0", "date": "2026-07-04T11:29:03.000Z", "commit": "17b462cd6d1e551cda340dc26e890ce88e86a313", "fileid": "https://r2.ropensci.org/e40f06526aa3406a27434bab5fc2c41082729b158800b11b50d0c371404d7dca", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704586639" }, { "r": "4.6.0", "os": "wasm", "version": "1.35.0", "date": "2026-07-04T11:30:21.000Z", "commit": "17b462cd6d1e551cda340dc26e890ce88e86a313", "fileid": "https://r2.ropensci.org/746c497502de619a367d786704b28f6228cea6ece9a3bde99e6c9417870b1c95", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704586639" }, { "r": "4.7.0", "os": "win", "version": "1.35.0", "date": "2026-07-04T11:28:21.000Z", "commit": "17b462cd6d1e551cda340dc26e890ce88e86a313", "fileid": "https://r2.ropensci.org/63941f970f1473faf87c6913160250415e4f4665a34d0195d23a0d821213d30f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704586639" }, { "r": "4.5.3", "os": "win", "version": "1.35.0", "date": "2026-07-04T11:28:29.000Z", "commit": "17b462cd6d1e551cda340dc26e890ce88e86a313", "fileid": "https://r2.ropensci.org/40e709c4426e5e2e6a2dd74a4b1592229b406813061e009ffed91171b1b780be", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704586639" }, { "r": "4.6.1", "os": "win", "version": "1.35.0", "date": "2026-07-04T11:28:24.000Z", "commit": "17b462cd6d1e551cda340dc26e890ce88e86a313", "fileid": "https://r2.ropensci.org/a54c936f5462062379d207b58a9e7438bd640b415debfcce86f73dfe9332fa9b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704586639" } ] }