{
  "_id": "6a19427aacfb0bcc41dd7d52",
  "Package": "DSS",
  "Title": "Dispersion shrinkage for sequencing data",
  "Version": "2.60.0",
  "Date": "2026-4-9",
  "Author": "Hao Wu<hao.wu@emory.edu>, Hao Feng<hxf155@case.edu>",
  "Maintainer": "Hao Wu <hao.wu@emory.edu>, Hao Feng <hxf155@case.edu>",
  "Description": "DSS is an R library performing differntial analysis for\ncount-based sequencing data. It detectes differentially\nexpressed genes (DEGs) from RNA-seq, and differentially\nmethylated loci or regions (DML/DMRs) from bisulfite sequencing\n(BS-seq). The core of DSS is a new dispersion shrinkage method\nfor estimating the dispersion parameter from Gamma-Poisson or\nBeta-Binomial distributions.",
  "License": "GPL",
  "VignetteBuilder": "knitr",
  "biocViews": "Sequencing, RNASeq, DNAMethylation,GeneExpression,\nDifferentialExpression,DifferentialMethylation",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:36 UTC",
  "RemoteUrl": "https://github.com/bioc/DSS",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "a954918494c51ec343aa885105c0b80ec69e4631",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-29 06:37:33 UTC",
    "User": "root"
  },
  "MD5sum": "d222937e5bf878e419760fc38803fbac",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "DSS_2.60.0.tar.gz",
  "_fileid": "46d7570d732a6fab16357aee851d5055c7b58ec7c91016b8cefe38afcd3432ee",
  "_filesize": 2005203,
  "_sha256": "46d7570d732a6fab16357aee851d5055c7b58ec7c91016b8cefe38afcd3432ee",
  "_created": "2026-05-29T06:37:33.000Z",
  "_published": "2026-05-29T07:38:34.507Z",
  "_jobs": [
    {
      "job": 78450923182,
      "time": 215,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7284691337"
    },
    {
      "job": 78450923253,
      "time": 304,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7284711879"
    },
    {
      "job": 78450923231,
      "time": 382,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7284729610"
    },
    {
      "job": 78450923218,
      "time": 323,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7284716452"
    },
    {
      "job": 78450923241,
      "time": 416,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7284737875"
    },
    {
      "job": 78450923272,
      "time": 250,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7285439389"
    },
    {
      "job": 78450923273,
      "time": 575,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7285544944"
    },
    {
      "job": 78450923198,
      "time": 213,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7285426795"
    },
    {
      "job": 78450923234,
      "time": 664,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7285564154"
    },
    {
      "job": 78450328825,
      "time": 296,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284641345"
    },
    {
      "job": 78450923178,
      "time": 135,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284672499"
    },
    {
      "job": 78450923219,
      "time": 370,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7284727208"
    },
    {
      "job": 78450923229,
      "time": 361,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7284725046"
    },
    {
      "job": 78450923230,
      "time": 310,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7284713356"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 17
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/DSS",
  "_commit": {
    "id": "a954918494c51ec343aa885105c0b80ec69e4631",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379796
  },
  "_maintainer": {
    "name": "Hao Wu",
    "email": "hxf155@case.edu",
    "login": "haowulab",
    "description": "Distinguished Professor in Artificial Intelligence ",
    "uuid": 16678455
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "BiocParallel",
      "role": "Depends"
    },
    {
      "package": "bsseq",
      "role": "Depends"
    },
    {
      "package": "parallel",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "splines",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "edgeR",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 4,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-15",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.61.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.60.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencing",
    "rnaseq",
    "dnamethylation",
    "geneexpression",
    "differentialexpression",
    "differentialmethylation"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 1374,
    "source": "https://www.bioconductor.org/packages/stats/bioc/DSS"
  },
  "_mentions": 288,
  "_searchresults": 330,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DSS.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "callDML",
    "callDMR",
    "dispersion",
    "dispersion<-",
    "DMLfit.multiFactor",
    "DMLtest",
    "DMLtest.multiFactor",
    "DSS.DE",
    "estDispersion",
    "estNormFactors",
    "makeBSseqData",
    "newSeqCountSet",
    "normalizationFactor",
    "normalizationFactor<-",
    "showOneDMR",
    "waldTest"
  ],
  "_datasets": [
    {
      "name": "design",
      "title": "Experimental design for the example RRBS dataset",
      "object": "RRBS",
      "file": "RRBS.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "case",
        "cell"
      ],
      "rows": 16,
      "table": true,
      "tojson": true
    },
    {
      "name": "RRBS",
      "title": "An example dataset for multiple factor design",
      "object": "RRBS",
      "file": "RRBS.RData",
      "class": [
        "BSseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "seqData",
      "title": "A simulated 'SeqCountData' object.",
      "object": "seqData",
      "file": "seqData.rda",
      "class": [
        "SeqCountSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "DSS-package",
      "title": "Dispersion shrinkage for sequencing data",
      "topics": [
        "DSS-package",
        "DSS"
      ]
    },
    {
      "page": "callDML",
      "title": "Function to detect differntially methylated loci (DML) from bisulfite sequencing (BS-seq) data.",
      "topics": [
        "callDML"
      ]
    },
    {
      "page": "callDMR",
      "title": "Function to detect differntially methylated regions (DMR) from bisulfite sequencing (BS-seq) data.",
      "topics": [
        "callDMR"
      ]
    },
    {
      "page": "design",
      "title": "Experimental design for the example RRBS dataset",
      "topics": [
        "design"
      ]
    },
    {
      "page": "dispersion",
      "title": "Acessor functions for the 'dispersion' slot in a SeqCountData object.",
      "topics": [
        "dispersion",
        "dispersion,SeqCountSet-method",
        "dispersion<-",
        "dispersion<-,SeqCountSet,numeric-method"
      ]
    },
    {
      "page": "DMLfit.multiFactor",
      "title": "Fit a linear model for BS-seq data from general experimental design",
      "topics": [
        "DMLfit.multiFactor"
      ]
    },
    {
      "page": "DMLtest",
      "title": "Function to perform statistical test of differntially methylated loci (DML) for two group comparisons of bisulfite sequencing (BS-seq) data.",
      "topics": [
        "DMLtest"
      ]
    },
    {
      "page": "DMLtest.multiFactor",
      "title": "Perform statistical test for BS-seq data from general experimental design",
      "topics": [
        "DMLtest.multiFactor"
      ]
    },
    {
      "page": "DSS.DE",
      "title": "Perform RNA-seq differential expression analysis in two-group comparison",
      "topics": [
        "DSS.DE"
      ]
    },
    {
      "page": "estDispersion",
      "title": "Estimate and shrink tag-specific dipsersions",
      "topics": [
        "estDispersion",
        "estDispersion,SeqCountSet-method"
      ]
    },
    {
      "page": "estNormFactors",
      "title": "Estimate normalization factors",
      "topics": [
        "estNormFactors",
        "estNormFactors,SeqCountSet-method"
      ]
    },
    {
      "page": "makeBSseqData",
      "title": "Create an object of BSseq class from several data frames.",
      "topics": [
        "makeBSseqData"
      ]
    },
    {
      "page": "normalizationFactor",
      "title": "Accessor functions for the 'normalizationFactor' slot in a SeqCountData object.",
      "topics": [
        "normalizationFactor",
        "normalizationFactor,SeqCountSet-method",
        "normalizationFactor<-",
        "normalizationFactor<-,SeqCountSet,matrix-method",
        "normalizationFactor<-,SeqCountSet,numeric-method"
      ]
    },
    {
      "page": "RRBS",
      "title": "An example dataset for multiple factor design",
      "topics": [
        "RRBS"
      ]
    },
    {
      "page": "SeqCountSet-class",
      "title": "Class '\"SeqCountSet\"' - container for count data from sequencing experiment",
      "topics": [
        "newSeqCountSet",
        "SeqCountSet",
        "SeqCountSet-class"
      ]
    },
    {
      "page": "seqData",
      "title": "A simulated 'SeqCountData' object.",
      "topics": [
        "seqData"
      ]
    },
    {
      "page": "showOneDMR",
      "title": "Visualze the count data for one DMR",
      "topics": [
        "showOneDMR"
      ]
    },
    {
      "page": "waldTest",
      "title": "Perform gene-wise Wald test for two group comparisons for sequencing count data.",
      "topics": [
        "waldTest",
        "waldTest,SeqCountSet-method"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "askpass",
    "assorthead",
    "beachmat",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "BSgenome",
    "bsseq",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DelayedArray",
    "DelayedMatrixStats",
    "dir.expiry",
    "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": "DSS.Rmd",
      "filename": "DSS.html",
      "title": "The DSS User's Guide",
      "author": "Hao Wu, hao.wu@emory.edu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Background",
        "Citation",
        "Using DSS for RNA-seq differential expression analysis",
        "Input data preparation",
        "Single factor experiment",
        "Multifactor experiment",
        "Using DSS for BS-seq differential methylation analysis",
        "Overview",
        "DML/DMR detection from two-group comparison",
        "Parallel computing for DML/DMR detection from two-group comparison",
        "DML/DMR detection from general experimental design",
        "Hypothesis testing in general experimental design",
        "Example analysis for data from general experimental design",
        "More flexible way to construct a hypothesis test",
        "For paired design",
        "Frequently Asked Questions",
        "For BS-seq data analysis",
        "Session Info",
        "References"
      ],
      "created": "2019-04-26 02:13:35",
      "modified": "2022-08-02 13:02:15",
      "commits": 11
    }
  ],
  "_score": 7.212803173368707,
  "_indexed": false,
  "_nocasepkg": "dss",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/DSS",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.60.0",
      "date": "2026-05-29T06:40:41.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "c54e203bd904fe2a944c5de3dbf0f9d49a9d05a7e2630b89323e41fd2acf4380",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.60.0",
      "date": "2026-05-29T06:41:34.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "9fc26df9cced0885f38e77f128bfe098339d8e59880867a199d8cfc8cb1536c4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.60.0",
      "date": "2026-05-29T06:40:51.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "7309b7a5a9a1e9bf722f1388890011e330bedc3a9d3adcfb9842d2b002aca38b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.60.0",
      "date": "2026-05-29T06:41:40.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "54a7b5155377389028c1093ff80b2773884a0bd8716369faeb0b245566cf7ed5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.60.0",
      "date": "2026-05-29T07:28:08.000Z",
      "arch": "aarch64",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "2de5bf479e109f8da67516d1aa793c74e5a2d5956f3f12b6aba3f4797e4656c4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.60.0",
      "date": "2026-05-29T07:30:59.000Z",
      "arch": "x86_64",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "55a324255259540ff336eb9306c514232ce13822d1ac4ce9173c618a793bcc75",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.60.0",
      "date": "2026-05-29T07:28:03.000Z",
      "arch": "aarch64",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "d8f79688e9e18c2b9b8c7364c4d47495f6605e1aa7e7bed3625eaacfef899258",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.60.0",
      "date": "2026-05-29T07:31:42.000Z",
      "arch": "x86_64",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "c7e91469857ecb97657f621116d9707b29a170e85462a0d2512b9afd54f11062",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.60.0",
      "date": "2026-05-29T06:40:35.000Z",
      "arch": "emscripten",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "4ee233dbc3075098b1912fb66e411c7a77156e3ea65cf6a42593a71c6c6ee028",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.60.0",
      "date": "2026-05-29T06:40:08.000Z",
      "arch": "x86_64",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "c7143918d23ffe2e9dec714deb12680eb9ec686450b4a37aadfa11e56c71ea16",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.60.0",
      "date": "2026-05-29T06:40:41.000Z",
      "arch": "x86_64",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "57ca6a583baed992becfdf07d423bcfae327d5256a276a7c0cba0a7e9968e691",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.60.0",
      "date": "2026-05-29T06:39:53.000Z",
      "arch": "x86_64",
      "commit": "a954918494c51ec343aa885105c0b80ec69e4631",
      "fileid": "caa94da627dbee23f831295c0e1fb804876a4442017d5784c408e8516579f475",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622121671"
    }
  ]
}