{
  "_id": "6a49428018cdde069385e639",
  "Package": "scmeth",
  "Type": "Package",
  "Title": "Functions to conduct quality control analysis in methylation\ndata",
  "Version": "1.33.0",
  "Author": "Divy Kangeyan <divyswar01@g.harvard.edu>",
  "Maintainer": "Divy Kangeyan <divyswar01@g.harvard.edu>",
  "Description": "Functions to analyze methylation data can be found here.\nSome functions are relevant for single cell methylation data\nbut most other functions can be used for any methylation data.\nHighlight of this workflow is the comprehensive quality control\nreport.",
  "biocViews": "DNAMethylation, QualityControl, Preprocessing, SingleCell,\nImmunoOncology",
  "BugReports": "https://github.com/aryeelab/scmeth/issues",
  "License": "GPL-2",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev libx11-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:18 UTC",
  "RemoteUrl": "https://github.com/bioc/scmeth",
  "RemoteRef": "HEAD",
  "RemoteSha": "f2ec0ad6754a7ae0f7db4480cf06eacb2a3052b9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 09:25:35 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "scmeth_1.33.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/557154947a9f26ff0c19db87eee89cb7a581623d120e55786c5fd466bd04d429",
  "_filesize": 845525,
  "_sha256": "557154947a9f26ff0c19db87eee89cb7a581623d120e55786c5fd466bd04d429",
  "_expires": "2026-10-12T17:27:26.000Z",
  "_created": "2026-07-04T09:25:35.000Z",
  "_published": "2026-07-04T17:27:28.674Z",
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 8
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28701692286",
  "_status": "success",
  "_upstream": "https://github.com/bioc/scmeth",
  "_commit": {
    "id": "f2ec0ad6754a7ae0f7db4480cf06eacb2a3052b9",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380438
  },
  "_maintainer": {
    "name": "Divy Kangeyan",
    "email": "divyswar01@g.harvard.edu"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85152167411,
      "time": 358,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8080489022"
    },
    {
      "job": 85152167519,
      "time": 639,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8080522987"
    },
    {
      "job": 85152167467,
      "time": 685,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8080526344"
    },
    {
      "job": 85152167447,
      "time": 460,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8080863410"
    },
    {
      "job": 85152167526,
      "time": 410,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8080863419"
    },
    {
      "job": 85152167180,
      "time": 506,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8080443673"
    },
    {
      "job": 85152167386,
      "time": 368,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8080493010"
    },
    {
      "job": 85152167482,
      "time": 499,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8080505859"
    },
    {
      "job": 85152167600,
      "time": 572,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8080512640"
    },
    {
      "job": 85152167487,
      "time": 515,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8080507620"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "bsseq",
      "role": "Imports"
    },
    {
      "package": "AnnotationHub",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BSgenome",
      "role": "Imports"
    },
    {
      "package": "DelayedArray",
      "version": ">= 0.5.15",
      "role": "Imports"
    },
    {
      "package": "annotatr",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "version": ">= 1.5.6",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "HDF5Array",
      "version": ">= 1.7.5",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Mmusculus.UCSC.mm10",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Hsapiens.NCBI.GRCh38",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg38.knownGene",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "Biobase",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "ggthemes",
      "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": "1.33.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "dnamethylation",
    "qualitycontrol",
    "preprocessing",
    "singlecell",
    "immunooncology",
    "bioconductor-package",
    "methylation",
    "single-cell-methylation"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "divy-kangeyan",
      "count": 274,
      "uuid": 8461629
    },
    {
      "user": "martinaryee",
      "count": 13,
      "uuid": 1827011
    },
    {
      "user": "nturaga",
      "count": 2,
      "uuid": 2746443
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "link-ny",
      "count": 1,
      "uuid": 4392950
    },
    {
      "user": "ajdunford",
      "count": 1,
      "uuid": 4085800
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/aryeelab/scmeth",
  "_searchresults": 8,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/scmeth.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/aryeelab/scmeth",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bsConversionPlot",
    "chromosomeCoverage",
    "coverage",
    "cpgDensity",
    "cpgDiscretization",
    "downsample",
    "featureCoverage",
    "mbiasplot",
    "methylationDist",
    "readmetrics",
    "repMask",
    "report"
  ],
  "_help": [
    {
      "page": "bsConversionPlot",
      "title": "Bisulfite conversion rate visualization",
      "topics": [
        "bsConversionPlot"
      ]
    },
    {
      "page": "chromosomeCoverage",
      "title": "CpG covergae in each chromosome",
      "topics": [
        "chromosomeCoverage"
      ]
    },
    {
      "page": "coverage",
      "title": "Coverage for single cells",
      "topics": [
        "coverage"
      ]
    },
    {
      "page": "cpgDensity",
      "title": "Provides Coverage by the CpG density. CpG Density is defined as the number of CpGs observed in certain base pair long region.",
      "topics": [
        "cpgDensity"
      ]
    },
    {
      "page": "cpgDiscretization",
      "title": "Discretize the CpG methylation values to align with single cell analysis",
      "topics": [
        "cpgDiscretization"
      ]
    },
    {
      "page": "downsample",
      "title": "Downsample analysis",
      "topics": [
        "downsample"
      ]
    },
    {
      "page": "featureCoverage",
      "title": "Coverage based on the genomic feature",
      "topics": [
        "featureCoverage"
      ]
    },
    {
      "page": "mbiasplot",
      "title": "Methylation bias plot",
      "topics": [
        "mbiasplot"
      ]
    },
    {
      "page": "methylationDist",
      "title": "Provide graphics for methylation distribution",
      "topics": [
        "methylationDist"
      ]
    },
    {
      "page": "readmetrics",
      "title": "Provide graphics for read information",
      "topics": [
        "readmetrics"
      ]
    },
    {
      "page": "repMask",
      "title": "Provides Coverage metrics in the repeat masker region",
      "topics": [
        "repMask"
      ]
    },
    {
      "page": "report",
      "title": "Generates an inclusive report on methylation analysis",
      "topics": [
        "report"
      ]
    },
    {
      "page": "scmeth",
      "title": "scmeth: a package to conduct quality control analysis for methylation data. Most functions can be applied to both bulk and single-cell methylation while other functions are specific to single-cell methylation data. scmeth is especially customized to use the output from the FireCloud implementation of methylation pipeline to produce comprehensive quality control report",
      "topics": [
        "scmeth-package",
        "scmeth"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/scmeth/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationHub",
    "annotatr",
    "askpass",
    "assorthead",
    "base64enc",
    "beachmat",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "bslib",
    "bsseq",
    "cachem",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "DelayedMatrixStats",
    "digest",
    "dir.expiry",
    "dplyr",
    "DT",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "gtools",
    "h5mread",
    "HDF5Array",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "otel",
    "permute",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "promises",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "readr",
    "regioneR",
    "reshape2",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "tzdb",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "my-vignette.Rmd",
      "filename": "my-vignette.html",
      "title": "scmeth Vignette",
      "author": "Divy S. Kangeyan",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Contents",
        "4.1 Report",
        "4.2 Functions",
        "readmetrics",
        "repmask",
        "Coverage by Chromosome",
        "featureCoverage",
        "cpgDensity",
        "downsample",
        "mbiasPlot",
        "methylationDist",
        "bsConversionPlot"
      ],
      "created": "2017-03-28 15:06:44",
      "modified": "2019-01-09 20:08:41",
      "commits": 48
    }
  ],
  "_score": 4.8750612633917,
  "_indexed": true,
  "_nocasepkg": "scmeth",
  "_universes": [
    "bioc",
    "aryeelab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-07-04T09:32:48.000Z",
      "distro": "resolute",
      "commit": "f2ec0ad6754a7ae0f7db4480cf06eacb2a3052b9",
      "fileid": "https://r2.ropensci.org/b25bb0dca1ccb463321943eba7287a2ce58b05ede65031d47fc02bb6ebd8b0b8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701692286"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-07-04T09:33:16.000Z",
      "distro": "resolute",
      "commit": "f2ec0ad6754a7ae0f7db4480cf06eacb2a3052b9",
      "fileid": "https://r2.ropensci.org/8e3b5a1df80ca3df0c3287d91d1162f1c986006d9fd52ed31b34695c2b04277a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701692286"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-07-04T10:23:55.000Z",
      "commit": "f2ec0ad6754a7ae0f7db4480cf06eacb2a3052b9",
      "fileid": "https://r2.ropensci.org/6b2357a744abfef06303f401fdfd5be5a9327408db7e7211974b04c7b2d41eae",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701692286"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-07-04T10:24:11.000Z",
      "commit": "f2ec0ad6754a7ae0f7db4480cf06eacb2a3052b9",
      "fileid": "https://r2.ropensci.org/d26d10f0c5304c2b2025e06a1b83349f52ca389deb3e8e9ab93ebe66288d298c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701692286"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.33.0",
      "date": "2026-07-04T09:33:26.000Z",
      "commit": "f2ec0ad6754a7ae0f7db4480cf06eacb2a3052b9",
      "fileid": "https://r2.ropensci.org/dd152c9d5dccc201aa69c3c631a82aa6accf6050b6e5a7e257520a3db6aa7977",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701692286"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T09:30:14.000Z",
      "commit": "f2ec0ad6754a7ae0f7db4480cf06eacb2a3052b9",
      "fileid": "https://r2.ropensci.org/c911eb1f36776f0fdc7124681dc1bbf5dd7068ea35503c2324c58c7abdb36d22",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701692286"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T09:30:35.000Z",
      "commit": "f2ec0ad6754a7ae0f7db4480cf06eacb2a3052b9",
      "fileid": "https://r2.ropensci.org/e0869622d5c0d29fd1829fcc3c9dec4b350a524832b992b4972974ecea43669b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701692286"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T09:30:19.000Z",
      "commit": "f2ec0ad6754a7ae0f7db4480cf06eacb2a3052b9",
      "fileid": "https://r2.ropensci.org/eda151c44e4a9dc9bf67510d6a3e93bcd59e9094ab19839b35c605af4d8e9cd7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701692286"
    }
  ]
}