{ "_id": "6a1ae3421d7bb097a09eec59", "Package": "methylKit", "Type": "Package", "Title": "DNA methylation analysis from high-throughput bisulfite\nsequencing results", "Version": "1.39.0", "Author": "Altuna Akalin [aut, cre], Matthias Kormaksson [aut], Sheng Li\n[aut], Arsene Wabo [ctb], Adrian Bierling [aut], Alexander\nBlume [aut], Katarzyna Wreczycka [ctb]", "Maintainer": "Altuna Akalin , Alexander Blume\n", "Description": "methylKit is an R package for DNA methylation analysis and\nannotation from high-throughput bisulfite sequencing. The\npackage is designed to deal with sequencing data from RRBS and\nits variants, but also target-capture methods and whole genome\nbisulfite sequencing. It also has functions to analyze\nbase-pair resolution 5hmC data from experimental protocols such\nas oxBS-Seq and TAB-Seq. Methylation calling can be performed\ndirectly from Bismark aligned BAM files.", "License": "Artistic-2.0", "URL": "https://github.com/al2na/methylKit", "BugReports": "https://github.com/al2na/methylKit/issues", "LazyLoad": "yes", "NeedsCompilation": "yes", "SystemRequirements": "GNU make", "biocViews": "DNAMethylation, Sequencing, MethylSeq", "VignetteBuilder": "knitr", "Collate": "'methylKit.R' 'backbone.R' 'diffMeth.R' 'clusterSamples.R'\n'regionalize.R' 'processBismarkAln.R' 'RcppExports.R'\n'document_data.R' 'bedgraph.R' 'reorganize.R'\n'percMethylation.R' 'normalizeCoverage.R' 'pool.R'\n'adjustMethylC.R' 'updateMethObject.R' 'batchControl.R'\n'dataSim.R' 'methylDBClasses.R' 'methylDBFunctions.R'\n'tabix.functions.R' 'methSeg.R' 'diffMethDSS.R'\n'deprecated_defunct.R' 'onUnload.R'", "RoxygenNote": "7.1.1", "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 12:43:51 UTC", "RemoteUrl": "https://github.com/bioc/methylKit", "RemoteRef": "HEAD", "RemoteSha": "ac7f68d4b40ea0dd51073db8085a68b51544d748", "Packaged": { "Date": "2026-05-30 09:33:03 UTC", "User": "root" }, "MD5sum": "85ce8fc5aa306bc660b463c6988b4a9b", "_user": "bioc", "_type": "src", "_file": "methylKit_1.39.0.tar.gz", "_fileid": "09c633e002b0221445b9af0efcd8aa05928e4dabc39a1cbc8d18669daeaa5ab9", "_filesize": 1469257, "_sha256": "09c633e002b0221445b9af0efcd8aa05928e4dabc39a1cbc8d18669daeaa5ab9", "_created": "2026-05-30T09:33:03.000Z", "_published": "2026-05-30T13:16:50.154Z", "_jobs": [ { "job": 78639939081, "time": 230, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307296044" }, { "job": 78639939120, "time": 384, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7307248685" }, { "job": 78639939109, "time": 482, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307320579" }, { "job": 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"time": 483, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307321320" }, { "job": 78639939104, "time": 509, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307323997" }, { "job": 78639939093, "time": 436, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307314211" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 18 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675666074", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/methylKit", "_commit": { "id": "ac7f68d4b40ea0dd51073db8085a68b51544d748", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380231 }, "_maintainer": { "name": "Altuna Akalin", "email": "alex.gos90@gmail.com", "login": "al2na", "twitter": "@AltunaAkalin", "description": "doing stuff ", "uuid": 638225 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "GenomicRanges", "version": ">= 1.18.1", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rhtslib", "version": ">= 1.13.1", "role": "LinkingTo" }, { "package": "IRanges", "role": "Imports" }, { "package": "data.table", "version": ">= 1.9.6", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.13.13", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "KernSmooth", "role": "Imports" }, { "package": "qvalue", "role": "Imports" }, { "package": "emdbook", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "gtools", "role": "Imports" }, { "package": "fastseg", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "mclust", "role": "Imports" }, { "package": 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"statistical-analysis", "visualization", "curl", "bzip2", "xz-utils", "zlib", "cpp" ], "_stars": 253, "_contributors": [ { "user": "alexg9010", "count": 353, "uuid": 14021775 }, { "user": "al2na", "count": 283, "uuid": 638225 }, { "user": "shengli", "count": 28, "uuid": 1214746 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 10, "uuid": 1744257 }, { "user": "hpages", "count": 7, "uuid": 8810451 }, { "user": "marcinkosinski", "count": 3, "uuid": 6773454 }, { "user": "katwre", "count": 3, "uuid": 11339547 }, { "user": "jondeen", "count": 2, "uuid": 763025 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "karl616", "count": 1, "uuid": 3873333 }, { "user": "lshep", "count": 1, "uuid": 18724380 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 1838, "source": "https://www.bioconductor.org/packages/stats/bioc/methylKit" }, "_mentions": 154, "_devurl": "https://github.com/al2na/methylkit", "_searchresults": 692, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/methylKit.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/al2na/methylkit", "_realowner": "bioc", "_cranurl": false, "_exports": [ "adjust.methylC", "adjustMethylC", "annotate.WithFeature", "annotate.WithFeature.Flank", "annotate.WithGenicParts", "assocComp", "bedgraph", "calculateDiffMeth", "calculateDiffMethDSS", "clusterSamples", "dataSim", "diffMethPerChr", "filterByCoverage", "get.methylDiff", "getAssembly", "getContext", "getCorrelation", "getCoverageStats", "getData", "getDBPath", "getFeatsWithTargetsStats", "getFlanks", "getMembers", "getMethylationStats", "getMethylDiff", "getSampleID", "getSampleID<-", "getTargetAnnotationStats", "getTreatment", "getTreatment<-", "joinSegmentNeighbours", "makeMethylDB", "methRead", "methSeg", "methSeg2bed", "methylRawList", "methylRawListDB", "normalizeCoverage", "PCASamples", "percMethylation", "plotTargetAnnotation", "pool", "processBismarkAln", "read", "read.bed", "read.bismark", "read.feature.flank", "read.transcript.features", "readMethylDB", "reconstruct", "regionCounts", "removeComp", "reorganize", "select", "selectByOverlap", "tileMethylCounts", "unite" ], "_datasets": [ { "name": "methylBase.obj", "title": "Example methylBase object.", "object": "methylKit", "file": "methylKit.RData", "class": [ "methylBase" ], "fields": [ "chr", "start", "end", "strand", "coverage1", "numCs1", "numTs1", "coverage2", "numCs2", "numTs2", "coverage3", "numCs3", "numTs3", "coverage4", "numCs4", "numTs4" ], "rows": 963, "table": true, "tojson": true }, { "name": "methylDiff.obj", "title": "Example methylKit objects.", "object": "methylKit", "file": "methylKit.RData", "class": [ "methylDiff" ], "fields": [ "chr", "start", "end", "strand", "pvalue", "qvalue", "meth.diff" ], "rows": 963, "table": true, "tojson": true }, { "name": "methylRawList.obj", "title": "Example methylRawList object.", "object": "methylKit", "file": "methylKit.RData", "class": [ "methylRawList" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "adjustMethylC", "title": "Adjust measured 5mC levels using 5hmC levels", "topics": [ "adjustMethylC", "adjustMethylC,methylRaw,methylRaw-method", "adjustMethylC,methylRawDB,methylRawDB-method", "adjustMethylC,methylRawList,methylRawList-method", "adjustMethylC,methylRawListDB,methylRawListDB-method" ] }, { "page": "assocComp-methods", "title": "Associate principal components with sample annotations", "topics": [ "assocComp" ] }, { "page": "bedgraph-methods", "title": "Get bedgraph from methylRaw, methylRawList and methylDiff objects", "topics": [ "bedgraph", "bedgraph,methylDiff-method", "bedgraph,methylDiffDB-method", "bedgraph,methylRaw-method", "bedgraph,methylRawDB-method", "bedgraph,methylRawList-method", "bedgraph,methylRawListDB-method" ] }, { "page": "calculateDiffMeth-methods", "title": "Calculate differential methylation statistics", "topics": [ "calculateDiffMeth", "calculateDiffMeth,methylBase-method", "calculateDiffMeth,methylBaseDB-method" ] }, { "page": "calculateDiffMethDSS-methods", "title": "calculate Differential Methylation with DSS", "topics": [ "calculateDiffMethDSS", "calculateDiffMethDSS,methylBase-method" ] }, { "page": "clusterSamples-methods", "title": "Hierarchical Clustering using methylation data The function clusters samples using 'hclust' function and various distance metrics derived from percent methylation per base or per region for each sample.", "topics": [ "clusterSamples", "clusterSamples,methylBase-method", "clusterSamples,methylBaseDB-method" ] }, { "page": "dataSim-methods", "title": "Simulate DNA methylation data", "topics": [ "dataSim" ] }, { "page": "diffMethPerChr-methods", "title": "Get and plot the number of hyper/hypo methylated regions/bases per chromosome", "topics": [ "diffMethPerChr", "diffMethPerChr,methylDiff-method", "diffMethPerChr,methylDiffDB-method" ] }, { "page": "extract-methods", "title": "extract parts of methylRaw,methylRawDB,methylBase,methylBaseDB and methylDiff data", "topics": [ "extract", "extract,methylBase,ANY-method", "extract,methylBaseDB,ANY-method", "extract,methylDiff,ANY-method", "extract,methylDiffDB,ANY-method", "extract,methylRaw,ANY-method", "extract,methylRawDB,ANY-method", "[,methylBase,ANY,ANY,ANY-method", "[,methylBaseDB,ANY,ANY,ANY-method", "[,methylDiff,ANY,ANY,ANY-method", "[,methylDiffDB,ANY,ANY,ANY-method", "[,methylRaw,ANY,ANY,ANY-method", "[,methylRawDB,ANY,ANY,ANY-method" ] }, { "page": "filterByCoverage-methods", "title": "Filter methylRaw, methylRawDB, methylRawList and methylRawListDB object based on read coverage", "topics": [ "filterByCoverage", "filterByCoverage,methylRaw-method", "filterByCoverage,methylRawDB-method", "filterByCoverage,methylRawList-method", "filterByCoverage,methylRawListDB-method" ] }, { "page": "getAssembly-methods", "title": "get assembly of the genome", "topics": [ "getAssembly", "getAssembly,methylBase-method", "getAssembly,methylBaseDB-method", "getAssembly,methylDiff-method", "getAssembly,methylDiffDB-method", "getAssembly,methylRaw-method", "getAssembly,methylRawDB-method" ] }, { "page": "getContext-methods", "title": "get the context of methylation", "topics": [ "getContext", "getContext,methylBase-method", "getContext,methylBaseDB-method", "getContext,methylDiff-method", "getContext,methylDiffDB-method", "getContext,methylRaw-method", "getContext,methylRawDB-method" ] }, { "page": "getCorrelation-methods", "title": "get correlation between samples in methylBase or methylBaseDB object", "topics": [ "getCorrelation", "getCorrelation,methylBase-method", "getCorrelation,methylBaseDB-method" ] }, { "page": "getCoverageStats-methods", "title": "get coverage stats from methylRaw object", "topics": [ "getCoverageStats", "getCoverageStats,methylRaw-method", "getCoverageStats,methylRawDB-method" ] }, { "page": "getData-methods", "title": "get the data slot from the methylKit objects", "topics": [ "getData", "getData,methylBase-method", "getData,methylBaseDB-method", "getData,methylDiff-method", "getData,methylDiffDB-method", "getData,methylRaw-method", "getData,methylRawDB-method" ] }, { "page": "getDBPath-methods", "title": "Get path to database of the methylDB objects", "topics": [ "getDBPath", "getDBPath,methylBaseDB-method", "getDBPath,methylDiffDB-method", "getDBPath,methylRawDB-method", "getDBPath,methylRawListDB-method" ] }, { "page": "getMethylationStats-methods", "title": "get Methylation stats from methylRaw or methylRawDB object", "topics": [ "getMethylationStats", "getMethylationStats,methylRaw-method", "getMethylationStats,methylRawDB-method" ] }, { "page": "getMethylDiff-methods", "title": "get differentially methylated regions/bases based on cutoffs", "topics": [ "getMethylDiff", "getMethylDiff,methylDiff-method", "getMethylDiff,methylDiffDB-method" ] }, { "page": "getSampleID-methods", "title": "Get or Set Sample-IDs of the methylKit objects", "topics": [ "getSampleID", "getSampleID,methylBase-method", "getSampleID,methylBaseDB-method", "getSampleID,methylDiff-method", "getSampleID,methylDiffDB-method", "getSampleID,methylRaw-method", "getSampleID,methylRawDB-method", "getSampleID,methylRawList-method", "getSampleID,methylRawListDB-method", "getSampleID<-", "getSampleID<-,methylBase-method", "getSampleID<-,methylBaseDB-method", "getSampleID<-,methylDiff-method", "getSampleID<-,methylDiffDB-method", "getSampleID<-,methylRaw-method", "getSampleID<-,methylRawDB-method", "getSampleID<-,methylRawList-method", "getSampleID<-,methylRawListDB-method" ] }, { "page": "getTreatment-methods", "title": "Get or Set treatment vector of methylKit object", "topics": [ "getTreatment", "getTreatment,getTreatment,methylDiffDB-method", "getTreatment,methylBase-method", "getTreatment,methylBaseDB-method", "getTreatment,methylDiff-method", "getTreatment,methylDiffDB-method", "getTreatment,methylRawList-method", "getTreatment,methylRawListDB-method", "getTreatment<-", "getTreatment<-,methylBase-method", "getTreatment<-,methylBaseDB-method", "getTreatment<-,methylDiff-method", "getTreatment<-,methylDiffDB-method", "getTreatment<-,methylRawList-method", "getTreatment<-,methylRawListDB-method" ] }, { "page": "joinSegmentNeighbours", "title": "Join directly neighbouring segments produced by methSeg", "topics": [ "joinSegmentNeighbours" ] }, { "page": "makeMethylDB-methods", "title": "coerce methylKit objects from memory to flat file database objects", "topics": [ "makeMethylDB", "makeMethylDB,methylBase-method", "makeMethylDB,methylBase-methods", "makeMethylDB,methylDiff-method", "makeMethylDB,methylDiff-methods", "makeMethylDB,methylRaw-method", "makeMethylDB,methylRaw-methods", "makeMethylDB,methylRawList-method", "makeMethylDB,methylRawList-methods" ] }, { "page": "methRead-methods", "title": "read file(s) to methylRaw or methylRawList objects", "topics": [ "methRead", "methRead,character,ANY,ANY-method", "methRead,character,character,character-method", "methRead,character-method", "methRead,list,ANY,ANY-method", "methRead,list,list,character-method" ] }, { "page": "methSeg", "title": "Segment methylation or differential methylation profile", "topics": [ "methSeg" ] }, { "page": "methSeg2bed", "title": "Export segments to BED files", "topics": [ "methSeg2bed" ] }, { "page": "methylBase-class", "title": "An S4 class for methylation events sampled in multiple experiments", "topics": [ "methylBase", "methylBase-class" ] }, { "page": "methylBase.obj", "title": "Example methylBase object.", "topics": [ "methylBase.obj" ] }, { "page": "methylBaseDB-class", "title": "An S4 class for storing methylation events sampled in multiple experiments as flat file database", "topics": [ "methylBaseDB", "methylBaseDB-class" ] }, { "page": "methylDiff-class", "title": "An S4 class that holds differential methylation information", "topics": [ "methylDiff", "methylDiff-class" ] }, { "page": "methylDiff.obj", "title": "Example methylKit objects.", "topics": [ "methylDiff.obj" ] }, { "page": "methylDiffDB-class", "title": "An S4 class that holds differential methylation information as flat file database", "topics": [ "methylDiffDB", "methylDiffDB-class" ] }, { "page": "methylKit-defunct", "title": "Deprecated/Defunct functions", "topics": [ "adjust.methylC", "annotate.WithFeature", "annotate.WithFeature.Flank", "annotate.WithGenicParts", "get.methylDiff", "getFeatsWithTargetsStats", "getFlanks", "getMembers", "getTargetAnnotationStats", "methylKit-defunct", "plotTargetAnnotation", "read", "read.bed", "read.bismark", "read.feature.flank", "read.transcript.features" ] }, { "page": "methylRaw-class", "title": "An S4 class for holding raw methylation data from an alignment pipeline.", "topics": [ "methylRaw", "methylRaw-class" ] }, { "page": "methylRawDB-class", "title": "An S4 class for storing raw methylation data as flat file database.", "topics": [ "methylRawDB", "methylRawDB-class" ] }, { "page": "methylRawList-class", "title": "An S4 class for holding a list of methylRaw objects.", "topics": [ "methylRawList", "methylRawList-class" ] }, { "page": "methylRawList.obj", "title": "Example methylRawList object.", "topics": [ "methylRawList.obj" ] }, { "page": "methylRawListDB-class", "title": "An S4 class for holding a list of methylRawDB objects.", "topics": [ "methylRawListDB", "methylRawListDB-class" ] }, { "page": "normalizeCoverage-methods", "title": "normalize read coverage between samples", "topics": [ "normalizeCoverage", "normalizeCoverage,methylRawList-method", "normalizeCoverage,methylRawListDB-method" ] }, { "page": "PCASamples-methods", "title": "Principal Components Analysis of Methylation data", "topics": [ "PCASamples", "PCASamples,methylBase-method", "PCASamples,methylBaseDB-method" ] }, { "page": "percMethylation-methods", "title": "get percent methylation scores from methylBase or methylBaseDB object", "topics": [ "percMethylation", "percMethylation,methylBase-method", "percMethylation,methylBaseDB-method" ] }, { "page": "pool-methods", "title": "Pool replicates within groups to a single sample per group", "topics": [ "pool", "pool,methylBase-method", "pool,methylBaseDB-method" ] }, { "page": "processBismarkAln-methods", "title": "Get methylation percentage from sorted Bismark alignments", "topics": [ "processBismarkAln", "processBismarkAln,character,character,character-method", "processBismarkAln,list,list,character-method" ] }, { "page": "readMethylDB-methods", "title": "load tabix file with header to methylDB", "topics": [ "readMethylDB" ] }, { "page": "reconstruct-methods", "title": "Reconstruct methylBase or methylBaseDB object based on a new methylation percentage matrix", "topics": [ "reconstruct", "reconstruct,ANY,methylBase-method", "reconstruct,ANY,methylBaseDB-method", "reconstruct,methylBase-method", "reconstruct,methylBaseDB-method" ] }, { "page": "regionCounts", "title": "Get regional counts for given GRanges or GRangesList object", "topics": [ "regionCounts", "regionCounts,methylBase,GRanges-method", "regionCounts,methylBase,GRangesList-method", "regionCounts,methylBaseDB,GRanges-method", "regionCounts,methylBaseDB,GRangesList-method", "regionCounts,methylRaw,GRanges-method", "regionCounts,methylRaw,GRangesList-method", "regionCounts,methylRawDB,GRanges-method", "regionCounts,methylRawDB,GRangesList-method", "regionCounts,methylRawList,GRanges-method", "regionCounts,methylRawList,GRangesList-method", "regionCounts,methylRawListDB,GRanges-method", "regionCounts,methylRawListDB,GRangesList-method" ] }, { "page": "removeComp-methods", "title": "Remove principal components from a methylBase object", "topics": [ "removeComp", "removeComp,methylBase-method", "removeComp,methylBaseDB-method" ] }, { "page": "reorganize-methods", "title": "Reorganize methylKit objects by creating new objects from subset of samples", "topics": [ "reorganize", "reorganize,methylBase-method", "reorganize,methylBaseDB-method", "reorganize,methylRawList-method", "reorganize,methylRawListDB-method" ] }, { "page": "select-methods", "title": "selects rows from of methylKit objects", "topics": [ "select", "select,methylBase-method", "select,methylBaseDB-method", "select,methylDiff-method", "select,methylDiffDB-method", "select,methylRaw-method", "select,methylRawDB-method" ] }, { "page": "selectByOverlap-methods", "title": "selects records of methylDB objects lying inside a GRanges range", "topics": [ "selectByOverlap", "selectByOverlap,methylBase,GRanges-method", "selectByOverlap,methylBase-method", "selectByOverlap,methylBaseDB,GRanges-method", "selectByOverlap,methylBaseDB-method", "selectByOverlap,methylDiff,GRanges-method", "selectByOverlap,methylDiff-method", "selectByOverlap,methylDiffDB,GRanges-method", "selectByOverlap,methylDiffDB-method", "selectByOverlap,methylRaw,GRanges-method", "selectByOverlap,methylRaw-method", "selectByOverlap,methylRawDB,GRanges-method", "selectByOverlap,methylRawDB-method", "selectByOverlap,methylRawList,GRanges-method", "selectByOverlap,methylRawList-method", "selectByOverlap,methylRawListDB,GRanges-method", "selectByOverlap,methylRawListDB-method" ] }, { "page": "show-methods", "title": "show method for methylKit classes", "topics": [ "show,methylBase", "show,methylBase-method", "show,methylBaseDB", "show,methylBaseDB-method", "show,methylDiff", "show,methylDiff-method", "show,methylDiffDB", "show,methylDiffDB-method", "show,methylRaw", "show,methylRaw-method", "show,methylRawDB", "show,methylRawDB-method", "show,methylRawList", "show,methylRawList-method", "show,methylRawListDB", "show,methylRawListDB-method" ] }, { "page": "tileMethylCounts-methods", "title": "Get methylated/unmethylated base counts for tilling windows", "topics": [ "tileMethylCounts", "tileMethylCounts,methylBase-method", "tileMethylCounts,methylBaseDB-method", "tileMethylCounts,methylRaw-method", "tileMethylCounts,methylRawDB-method", "tileMethylCounts,methylRawList-method", "tileMethylCounts,methylRawListDB-method" ] }, { "page": "unite-methods", "title": "unite methylRawList to a single table", "topics": [ "unite", "unite,methylRawList-method", "unite,methylRawListDB-method" ] }, { "page": "updateMethObject", "title": "update methylKit objects The method updates object from earlier versions (