{ "_id": "6a1539c2acfb0bcc41d509db", "Package": "methimpute", "Type": "Package", "Title": "Imputation-guided re-construction of complete methylomes from\nWGBS data", "Version": "1.35.0", "Author": "Aaron Taudt", "Maintainer": "Aaron Taudt ", "Description": "This package implements functions for calling methylation\nfor all cytosines in the genome.", "License": "Artistic-2.0", "LazyLoad": "yes", "VignetteBuilder": "knitr", "RoxygenNote": "6.1.1", "biocViews": "ImmunoOncology, Software, DNAMethylation, Epigenetics,\nHiddenMarkovModel, Sequencing, Coverage", "Config/pak/sysreqs": "libicu-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:46:35 UTC", "RemoteUrl": "https://github.com/bioc/methimpute", "RemoteRef": "HEAD", "RemoteSha": "a1c9caaca13714c82b736242019d86ee370a5aae", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-26 06:03:57 UTC", "User": "root" }, "MD5sum": "a669739d948b6b1a772174f239be2ddf", "_user": "bioc", "_type": "src", "_file": "methimpute_1.35.0.tar.gz", "_fileid": "b4a11a3b9d263d799295c85c549836f989316d94c285f5ef06fe6f2d4f0499df", "_filesize": 1472158, "_sha256": "b4a11a3b9d263d799295c85c549836f989316d94c285f5ef06fe6f2d4f0499df", "_created": "2026-05-26T06:03:57.000Z", "_published": "2026-05-26T06:12:18.047Z", "_jobs": [ { "job": 77816813700, "time": 193, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7210021664" }, { "job": 77816813723, "time": 226, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7210028654" }, { "job": 77816813778, "time": 261, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7210036208" }, { "job": 77816813717, "time": 241, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7210032092" }, { "job": 77816813731, "time": 272, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7210038290" }, { "job": 77816813737, "time": 198, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7210030205" }, { "job": 77816813739, "time": 336, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7210060861" }, { "job": 77816813734, "time": 143, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7210017085" }, { "job": 77816813720, "time": 410, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7210072161" }, { "job": 77816183178, "time": 337, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7209979370" }, { "job": 77816813693, "time": 138, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7210009711" }, { "job": 77816813755, "time": 235, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7210030676" }, { "job": 77816813692, "time": 194, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7210021744" }, { "job": 77816813705, "time": 211, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7210025511" } ], "_bioccheck": { "error": 1, "warning": 3, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/methimpute", "_commit": { "id": "a1c9caaca13714c82b736242019d86ee370a5aae", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380395 }, "_maintainer": { "name": "Aaron Taudt", "email": "aaron.taudt@gmail.com", "login": "ataudt", "linkedin": "in/aaron-taudt-4a837214b", "orcid": "0000-0002-9639-2306", "description": "Weaving code since 2003.", "uuid": 7465392 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "ggplot2", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.4.5", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "minpack.lm", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "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": [ "immunooncology", "software", "dnamethylation", "epigenetics", "hiddenmarkovmodel", "sequencing", "coverage", "cpp", "openmp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 436, "source": "https://www.bioconductor.org/packages/stats/bioc/methimpute" }, "_mentions": 1, "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/methimpute.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "binCounts", "binMethylome", "binomialTestMethylation", "binPositions", "callMethylation", "callMethylationSeparate", "collapseBins", "distanceCorrelation", "estimateTransDist", "exportMethylome", "extractCytosinesFromFASTA", "getDistinctColors", "getStateColors", "importBismark", "importBSMAP", "importBSSeeker", "importMethylpy", "inflateMethylome", "loadFromFiles", "plotConvergence", "plotEnrichment", "plotHistogram", "plotPosteriorDistance", "plotScatter", "plotTransitionProbs" ], "_datasets": [ { "name": "arabidopsis_chromosomes", "title": "Chromosome lengths for Arabidopsis", "object": "arabidopsis_chromosomes", "file": "arabidopsis_chromosomes.RData", "class": [ "data.frame" ], "fields": [ "chromosome", "length" ], "rows": 7, "table": true, "tojson": true }, { "name": "arabidopsis_genes", "title": "Gene coordinates for Arabidopsis (chr1)", "object": "arabidopsis_genes", "file": "arabidopsis_genes.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "arabidopsis_TEs", "title": "Transposable element coordinates for Arabidopsis (chr1)", "object": "arabidopsis_TEs", "file": "arabidopsis_TEs.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "arabidopsis_toydata", "title": "Toy data for Arabidopsis (200.000bp of chr1)", "object": "arabidopsis_toydata", "file": "arabidopsis_toydata.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "methimpute-package", "title": "methIMPUTE: Imputation-guided methylation status calling for WGBS-seq", "topics": [ "methimpute-package", "methimpute" ] }, { "page": "arabidopsis_chromosomes", "title": "Chromosome lengths for Arabidopsis", "topics": [ "arabidopsis_chromosomes" ] }, { "page": "arabidopsis_genes", "title": "Gene coordinates for Arabidopsis (chr1)", "topics": [ "arabidopsis_genes" ] }, { "page": "arabidopsis_TEs", "title": "Transposable element coordinates for Arabidopsis (chr1)", "topics": [ "arabidopsis_TEs" ] }, { "page": "arabidopsis_toydata", "title": "Toy data for Arabidopsis (200.000bp of chr1)", "topics": [ "arabidopsis_toydata" ] }, { "page": "binning", "title": "Methimpute binning functions", "topics": [ "binCounts", "binMethylome", "binning", "binPositions" ] }, { "page": "binomialTestMethylation", "title": "Call methylation status", "topics": [ "binomialTestMethylation" ] }, { "page": "callMethylation", "title": "Call methylation status", "topics": [ "callMethylation" ] }, { "page": "callMethylationSeparate", "title": "Call methylation status", "topics": [ "callMethylationSeparate" ] }, { "page": "collapseBins", "title": "Collapse consecutive bins", "topics": [ "collapseBins" ] }, { "page": "distanceCorrelation", "title": "Distance correlation", "topics": [ "distanceCorrelation" ] }, { "page": "estimateTransDist", "title": "'transDist' parameter", "topics": [ "estimateTransDist" ] }, { "page": "exportMethylome", "title": "Export a methylome", "topics": [ "exportMethylome" ] }, { "page": "extractCytosinesFromFASTA", "title": "Extract cytosine coordinates", "topics": [ "extractCytosinesFromFASTA" ] }, { "page": "getDistinctColors", "title": "Get distinct colors", "topics": [ "getDistinctColors" ] }, { "page": "getPosteriors", "title": "Get original posteriors", "topics": [ "getPosteriors" ] }, { "page": "getStateColors", "title": "Get state colors", "topics": [ "getStateColors" ] }, { "page": "import", "title": "Methimpute data import", "topics": [ "import", "importBismark", "importBSMAP", "importBSSeeker", "importMethylpy" ] }, { "page": "importRene", "title": "Import a Rene methylation extractor file", "topics": [ "importRene" ] }, { "page": "inflateMethylome", "title": "Inflate an imported methylation extractor file", "topics": [ "inflateMethylome" ] }, { "page": "loadFromFiles", "title": "Load 'methimpute' objects from file", "topics": [ "loadFromFiles" ] }, { "page": "methimpute-objects", "title": "methimpute objects", "topics": [ "methimpute-objects" ] }, { "page": "methimputeBinomialHMM", "title": "methimputeBinomialHMM", "topics": [ "methimputeBinomialHMM" ] }, { "page": "methimputeData", "title": "methimputeData", "topics": [ "methimputeData" ] }, { "page": "parameterScan", "title": "Perform a parameter scan", "topics": [ "parameterScan" ] }, { "page": "plotting", "title": "Methimpute plotting functions", "topics": [ "plotConvergence", "plotEnrichment", "plotHistogram", "plotPosteriorDistance", "plotScatter", "plotting", "plotTransitionProbs" ] }, { "page": "print.methimputeBinomialHMM", "title": "Print model object", "topics": [ "print.methimputeBinomialHMM" ] }, { "page": "transCoord", "title": "Transform genomic coordinates", "topics": [ "transCoord" ] } ], "_readme": "https://github.com/bioc/methimpute/raw/HEAD/README.md", "_rundeps": [ "askpass", "BiocGenerics", "Biostrings", "cli", "cpp11", "crayon", "curl", "data.table", "farver", "generics", "GenomeInfoDb", "GenomicRanges", "ggplot2", "glue", "gtable", "httr", "IRanges", "isoband", "jsonlite", "labeling", "lifecycle", "magrittr", "mime", "minpack.lm", "openssl", "plyr", "R6", "RColorBrewer", "Rcpp", "reshape2", "rlang", "S4Vectors", "S7", "scales", "Seqinfo", "stringi", "stringr", "sys", "UCSC.utils", "vctrs", "viridisLite", "withr", "XVector" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "methimpute.Rnw", "filename": "methimpute.pdf", "title": "Methylation status calling with METHimpute", "engine": "knitr::knitr", "headings": [], "created": "2017-02-06 08:39:41", "modified": "2018-06-12 07:26:47", "commits": 12 } ], "_score": 4.176091259055681, "_indexed": true, "_nocasepkg": "methimpute", "_universes": [ "bioc", "ataudt" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-05-26T06:06:49.000Z", "distro": "noble", "arch": "aarch64", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "d879ede8f2d101b6ea4a1dc76cf1308fac76d4c099f76ae1f3ba52a8b21f7a56", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" }, { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-05-26T06:07:02.000Z", "distro": "noble", "arch": "x86_64", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "b1fc9664974725295110ac81a389779651858afa8fb32fef870139a4c02fc770", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" }, { "r": "4.6.0", "os": "linux", "version": "1.35.0", "date": "2026-05-26T06:06:57.000Z", "distro": "noble", "arch": "aarch64", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "86215eeadc35a2e0c1ffd2ee09affc5d8d51f968eb7dc674d72135100ac267fd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" }, { "r": "4.6.0", "os": "linux", "version": "1.35.0", "date": "2026-05-26T06:07:24.000Z", "distro": "noble", "arch": "x86_64", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "66f08350a6603fd3a6ab5e09eddaf32cb680198179758edc0ad0df1f993f6272", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-05-26T06:06:57.000Z", "arch": "aarch64", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "f637a7e1187a07ba26d1d233bd52f78984b68920dd980db92038da6aaadaac6a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-05-26T06:08:08.000Z", "arch": "x86_64", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "545e14c35903d9e3fe3b1aeb51327ec01774db45543f04be08d37c81e56a6a6d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" }, { "r": "4.6.0", "os": "mac", "version": "1.35.0", "date": "2026-05-26T06:06:20.000Z", "arch": "aarch64", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "e2e46a9c79f065d03c02f211ed1295b4200aac23b9a7726ab438bc73b116e420", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" }, { "r": "4.6.0", "os": "mac", "version": "1.35.0", "date": "2026-05-26T06:07:52.000Z", "arch": "x86_64", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "07384e5074b989ad833a5b1ae9f7471b34e21019e1da4a403985490726146555", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" }, { "r": "4.6.0", "os": "wasm", "version": "1.35.0", "date": "2026-05-26T06:06:46.000Z", "arch": "emscripten", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "28e355cdbef415ce9ead8d7710c3cb6a90e21690c18d42eeb4394f1416af67b6", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" }, { "r": "4.7.0", "os": "win", "version": "1.35.0", "date": "2026-05-26T06:05:56.000Z", "arch": "x86_64", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "436af40eed4f7a0f65d1b3c977abada79f05b3cb2b21a60a4c658b4d6680936f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" }, { "r": "4.5.3", "os": "win", "version": "1.35.0", "date": "2026-05-26T06:05:53.000Z", "arch": "x86_64", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "1a99ca8aa10bf954b9eb9404447325a0da1edb0dc973be4d0c2f669aaed23f17", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" }, { "r": "4.6.0", "os": "win", "version": "1.35.0", "date": "2026-05-26T06:05:44.000Z", "arch": "x86_64", "commit": "a1c9caaca13714c82b736242019d86ee370a5aae", "fileid": "6c1f7b73ed258bfe8ba2c535e01da2b2edcfcad5b0cc8bd48c7831a527920a41", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435148880" } ] }