{ "_id": "6a4943bc18cdde069385ed65", "Package": "methylSig", "Title": "MethylSig: Differential Methylation Testing for WGBS and RRBS\nData", "Version": "1.25.0", "Date": "2025-07-28", "Authors@R": "c(person(given = \"Yongseok\",\nfamily = \"Park\",\nrole = \"aut\",\nemail = \"yongpark@pitt.edu\"),\nperson(given = \"Raymond G.\",\nfamily = \"Cavalcante\",\nrole = c(\"aut\", \"cre\"),\nemail = \"rcavalca@umich.edu\"))", "Description": "MethylSig is a package for testing for differentially\nmethylated cytosines (DMCs) or regions (DMRs) in whole-genome\nbisulfite sequencing (WGBS) or reduced representation bisulfite\nsequencing (RRBS) experiments. MethylSig uses a beta binomial\nmodel to test for significant differences between groups of\nsamples. Several options exist for either site-specific or\nsliding window tests, and variance estimation.", "License": "GPL-3", "BugReports": "https://github.com/sartorlab/methylSig/issues", "biocViews": "DNAMethylation, DifferentialMethylation, Epigenetics,\nRegression, MethylSeq", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.0", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:33 UTC", "RemoteUrl": "https://github.com/bioc/methylSig", "RemoteRef": "HEAD", "RemoteSha": "3cf80514e4f196e89208c2bd9353547324dc807d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 13:22:41 UTC", "User": "root" }, "Author": "Yongseok Park [aut],\nRaymond G. Cavalcante [aut, cre]", "Maintainer": "Raymond G. Cavalcante ", "_user": "bioc", "_type": "src", "_file": "methylSig_1.25.0.tar.gz", "_fileid": "https://r2.ropensci.org/f949a8231dc6f423b11eebbf6af58c2e40954dc747bf85304af73223888c34ca", "_filesize": 203232, "_sha256": "f949a8231dc6f423b11eebbf6af58c2e40954dc747bf85304af73223888c34ca", "_expires": "2026-10-12T17:32:42.000Z", "_created": "2026-07-04T13:22:41.000Z", "_published": "2026-07-04T17:32:43.990Z", "_bioccheck": { "error": 0, "warning": 0, "note": 9 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28707434518", "_status": "success", "_upstream": "https://github.com/bioc/methylSig", "_commit": { "id": "3cf80514e4f196e89208c2bd9353547324dc807d", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380753 }, "_maintainer": { "name": "Raymond G. Cavalcante", "email": "rcavalca@umich.edu", "login": "rcavalcante", "description": "", "uuid": 626455 }, "_distro": "resolute", "_jobs": [ { "job": 85152526816, "time": 260, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8082105094" }, { "job": 85152526961, "time": 508, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8082134137" }, { "job": 85152526874, "time": 507, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8082134050" }, { "job": 85152526966, "time": 233, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8082102310" }, { "job": 85152526963, "time": 313, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8082110987" }, { "job": 85152526693, "time": 358, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8082077284" }, { "job": 85152526748, "time": 237, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8082102866" }, { "job": 85152526861, "time": 432, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8082124473" }, { "job": 85152526972, "time": 396, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8082120435" }, { "job": 85152526970, "time": 462, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8082128359" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "bsseq", "role": "Imports" }, { "package": "DelayedArray", "role": "Imports" }, { "package": "DelayedMatrixStats", "role": "Imports" }, { "package": "DSS", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "bsseqData", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-31", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "dnamethylation", "differentialmethylation", "epigenetics", "regression", "methylseq", "differential-methylation", "dna-methylation" ], "_stars": 20, "_contributors": [ { "user": "rcavalcante", "count": 45, "uuid": 626455 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "jwokaty", "count": 8, "uuid": 1744257 }, { "user": "yongparkpitt", "count": 1, "uuid": 12517103 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 11, "_devurl": "https://github.com/sartorlab/methylsig", "_searchresults": 38, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/methylSig.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/sartorlab/methylsig", "_realowner": "bioc", "_cranurl": false, "_exports": [ "diff_binomial", "diff_dss_fit", "diff_dss_test", "diff_methylsig", "filter_loci_by_coverage", "filter_loci_by_group_coverage", "filter_loci_by_location", "tile_by_regions", "tile_by_windows" ], "_datasets": [ { "name": "bsseq_destranded", "title": "BSseq object read from destranded coverage files", "object": "bsseq_destranded", "class": [ "BSseq" ], "fields": [], "table": false, "tojson": false }, { "name": "bsseq_multichrom", "title": "BSseq object with loci on multiple chromosomes", "object": "bsseq_multichrom", "class": [ "BSseq" ], "fields": [], "table": false, "tojson": false }, { "name": "bsseq_stranded", "title": "BSseq object read from stranded coverage files", "object": "bsseq_stranded", "class": [ "BSseq" ], "fields": [], "table": false, "tojson": false }, { "name": "promoters_gr", "title": "GRanges object with collapsed promoters on chr21 and chr22", "object": "promoters_gr", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "bsseq_destranded", "title": "BSseq object read from destranded coverage files", "topics": [ "bsseq_destranded" ] }, { "page": "bsseq_multichrom", "title": "BSseq object with loci on multiple chromosomes", "topics": [ "bsseq_multichrom" ] }, { "page": "bsseq_stranded", "title": "BSseq object read from stranded coverage files", "topics": [ "bsseq_stranded" ] }, { "page": "diff_binomial", "title": "Differential methylation analysis using binomial model", "topics": [ "diff_binomial" ] }, { "page": "diff_dss_fit", "title": "Performs model fit for general experimental design", "topics": [ "diff_dss_fit" ] }, { "page": "diff_dss_test", "title": "Calculates differential methylation statistics under general experimental design", "topics": [ "diff_dss_test" ] }, { "page": "diff_methylsig", "title": "Calculates differential methylation statistics using a Beta-binomial approach", "topics": [ "diff_methylsig" ] }, { "page": "filter_loci_by_coverage", "title": "Filter BSseq object by coverage", "topics": [ "filter_loci_by_coverage" ] }, { "page": "filter_loci_by_group_coverage", "title": "Filter loci based on coverage threshold per sample per group", "topics": [ "filter_loci_by_group_coverage" ] }, { "page": "filter_loci_by_location", "title": "Remove loci by overlap with a 'GRanges' object", "topics": [ "filter_loci_by_location" ] }, { "page": "promoters_gr", "title": "GRanges object with collapsed promoters on chr21 and chr22", "topics": [ "promoters_gr" ] }, { "page": "tile_by_regions", "title": "Group cytosine / CpG level data into regions based on genomic regions", "topics": [ "tile_by_regions" ] }, { "page": "tile_by_windows", "title": "Group cytosine / CpG level data into regions based on genomic windows", "topics": [ "tile_by_windows" ] } ], "_readme": "https://github.com/bioc/methylSig/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "assorthead", "beachmat", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "biocmake", "BiocParallel", "Biostrings", "bitops", "BSgenome", "bsseq", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DelayedArray", "DelayedMatrixStats", "dir.expiry", "DSS", "farver", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "glue", "gtools", "h5mread", "HDF5Array", "httr", "IRanges", "jsonlite", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "Matrix", "MatrixGenerics", "matrixStats", "mime", "openssl", "permute", "R.methodsS3", "R.oo", "R.utils", "R6", "RColorBrewer", "Rcpp", "RCurl", "restfulr", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rjson", "rlang", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "scales", "Seqinfo", "snow", "SparseArray", "sparseMatrixStats", "statmod", "SummarizedExperiment", "sys", "viridisLite", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "updating-methylSig-code.Rmd", "filename": "updating-methylSig-code.html", "title": "Updating methylSig code", "author": "Raymond G. Cavalcante", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Reading Data", "Old methylSig", "New methylSig", "Tiling Data", "Testing", "MethylSig Test", "DSS Test", "Session Info" ], "created": "2020-03-23 14:10:34", "modified": "2020-03-23 14:10:34", "commits": 1 }, { "source": "using-methylSig.Rmd", "filename": "using-methylSig.html", "title": "Using methylSig", "author": "Yongseok Park, Raymond G. Cavalcante, Maria E. Figueroa, Laura S. Rozek, and Maureen A. Sartor", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Usage", "Reading Data", "Filtering Data", "By Coverage", "By Location", "Aggregating Data", "By Tiling the Genome", "By Pre-defined Regions", "Testing for Differential Methylation", "Filtering by Coverage in a Minimum Number of Samples", "Binomial Test", "MethylSig Test", "General Models with DSS", "Model Fitting", "Building Contrasts", "Testing", "Session Info" ], "created": "2020-03-23 14:10:34", "modified": "2020-03-23 14:10:34", "commits": 1 } ], "_score": 7.9599948383284165, "_indexed": true, "_nocasepkg": "methylsig", "_universes": [ "bioc", "rcavalcante", "sartorlab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-07-04T13:27:22.000Z", "distro": "resolute", "commit": "3cf80514e4f196e89208c2bd9353547324dc807d", "fileid": "https://r2.ropensci.org/1ed5a724067a736b1472bbadb43056201763b6b755a321ec973ec21c271b21f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707434518" }, { "r": "4.6.1", "os": "linux", "version": "1.25.0", "date": "2026-07-04T13:27:53.000Z", "distro": "resolute", "commit": "3cf80514e4f196e89208c2bd9353547324dc807d", "fileid": "https://r2.ropensci.org/7f1d66c2de7c90f4ba4ede23127ac4b11fc5db2ec2c435cc3c976898c0ab6be4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707434518" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-07-04T13:25:10.000Z", "commit": "3cf80514e4f196e89208c2bd9353547324dc807d", "fileid": "https://r2.ropensci.org/5ca739664418ebc468bf262981f8399038a651f4cded21b3edfe8827b7ee12d3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707434518" }, { "r": "4.6.1", "os": "mac", "version": "1.25.0", "date": "2026-07-04T13:25:29.000Z", "commit": "3cf80514e4f196e89208c2bd9353547324dc807d", "fileid": "https://r2.ropensci.org/baac3680f2d0c6b7ee1b900bb3e0d234a4ca5ceaf89e517250dca6d2b2b6296d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707434518" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-07-04T13:27:17.000Z", "commit": "3cf80514e4f196e89208c2bd9353547324dc807d", "fileid": "https://r2.ropensci.org/e92d0fa6e5eac87c0a93f937520ee11cc6300543e6a349026964622f7954ce77", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707434518" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-07-04T13:25:44.000Z", "commit": "3cf80514e4f196e89208c2bd9353547324dc807d", "fileid": "https://r2.ropensci.org/cb53217af6f3d9c38ab08ce8d3993dfc84effac5fe4feb2f0f59a39fdbbcc882", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707434518" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-07-04T13:25:42.000Z", "commit": "3cf80514e4f196e89208c2bd9353547324dc807d", "fileid": "https://r2.ropensci.org/5c5ca213710b786f12f1b56dfae0ad9cc44bf58fb903be0f5dc1fbb720fa79de", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707434518" }, { "r": "4.6.1", "os": "win", "version": "1.25.0", "date": "2026-07-04T13:26:06.000Z", "commit": "3cf80514e4f196e89208c2bd9353547324dc807d", "fileid": "https://r2.ropensci.org/08261e325560d7786d257015f9805c680204e31f5109aa47e3a6a9562568f010", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707434518" } ] }