{
  "_id": "6a49402f18cdde069385d9dc",
  "Package": "SIMD",
  "Type": "Package",
  "Title": "Statistical Inferences with MeDIP-seq Data (SIMD) to infer the\nmethylation level for each CpG site",
  "Version": "1.31.0",
  "Author": "Yan Zhou",
  "Maintainer": "Jiadi Zhu <2160090406@email.szu.edu.cn>",
  "Description": "This package provides a inferential analysis method for\ndetecting differentially expressed CpG sites in MeDIP-seq data.\nIt uses statistical framework and EM algorithm, to identify\ndifferentially expressed CpG sites. The methods on this package\nare described in the article 'Methylation-level Inferences and\nDetection of Differential Methylation with Medip-seq Data' by\nYan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chunfu Jiang\nand Xiyan Yang (2018, pending publication).",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "biocViews": "ImmunoOncology, DifferentialMethylation,SingleCell,\nDifferentialExpression",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "6.0.1",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:42 UTC",
  "RemoteUrl": "https://github.com/bioc/SIMD",
  "RemoteRef": "HEAD",
  "RemoteSha": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-04 05:57:08 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "SIMD_1.31.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/2b4f466d6789c7826bb37ab23420dc77e548d20139ca2d4c7b9f4814ba861821",
  "_filesize": 227209,
  "_sha256": "2b4f466d6789c7826bb37ab23420dc77e548d20139ca2d4c7b9f4814ba861821",
  "_expires": "2026-10-12T17:17:34.000Z",
  "_created": "2026-07-04T05:57:08.000Z",
  "_published": "2026-07-04T17:17:35.560Z",
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 11
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481",
  "_status": "success",
  "_upstream": "https://github.com/bioc/SIMD",
  "_commit": {
    "id": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
    "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": 1777380522
  },
  "_maintainer": {
    "name": "Jiadi Zhu",
    "email": "2160090406@email.szu.edu.cn",
    "login": "focuspaka",
    "description": "",
    "uuid": 40629719
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85151491531,
      "time": 142,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8078905630"
    },
    {
      "job": 85151491575,
      "time": 145,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8078906401"
    },
    {
      "job": 85151491573,
      "time": 182,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8078910464"
    },
    {
      "job": 85151491720,
      "time": 131,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8078904674"
    },
    {
      "job": 85151491576,
      "time": 175,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8078909494"
    },
    {
      "job": 85151491657,
      "time": 116,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8079192225"
    },
    {
      "job": 85151491664,
      "time": 166,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8078909267"
    },
    {
      "job": 85151491569,
      "time": 84,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8079186798"
    },
    {
      "job": 85151491455,
      "time": 153,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8078911155"
    },
    {
      "job": 85151491356,
      "time": 157,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8078888860"
    },
    {
      "job": 85151491574,
      "time": 108,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8078901738"
    },
    {
      "job": 85151491547,
      "time": 74,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8078897911"
    },
    {
      "job": 85151491488,
      "time": 88,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8078899707"
    },
    {
      "job": 85151491622,
      "time": 74,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8078897917"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "statmod",
      "role": "Imports"
    },
    {
      "package": "methylMnM",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.31.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "differentialmethylation",
    "singlecell",
    "differentialexpression"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 83,
  "_searchresults": 2,
  "_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/SIMD.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "EMalgorithm",
    "emalgth",
    "emalgth1",
    "EMtest",
    "probBinom"
  ],
  "_datasets": [
    {
      "name": "all_CpGsite_bin_chr18",
      "title": "A simulation dataset of CpG sites.",
      "object": "example_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4"
      ],
      "rows": 2000,
      "table": true,
      "tojson": true
    },
    {
      "name": "EM_H1ESB1_MeDIP_sigleCpG",
      "title": "A simulation dataset of MeDIP CpG sites.",
      "object": "example_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4"
      ],
      "rows": 2000,
      "table": true,
      "tojson": true
    },
    {
      "name": "EM2_H1ESB1_MeDIP_sigleCpG",
      "title": "A simulation dataset of MeDIP CpG sites.",
      "object": "example_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4"
      ],
      "rows": 2000,
      "table": true,
      "tojson": true
    },
    {
      "name": "EM2_H1ESB2_MeDIP_sigleCpG",
      "title": "A simulation dataset of MeDIP CpG sites.",
      "object": "example_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4"
      ],
      "rows": 2000,
      "table": true,
      "tojson": true
    },
    {
      "name": "H1ESB1_MRE_sigleCpG",
      "title": "A simulation dataset of MRE CpG sites.",
      "object": "example_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4"
      ],
      "rows": 2000,
      "table": true,
      "tojson": true
    },
    {
      "name": "H1ESB2_MRE_sigleCpG",
      "title": "A simulation dataset of MRE CpG sites.",
      "object": "example_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4"
      ],
      "rows": 2000,
      "table": true,
      "tojson": true
    },
    {
      "name": "three_mre_cpg",
      "title": "A simulation dataset of MRE CpG sites.",
      "object": "example_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4"
      ],
      "rows": 2000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "SIMD-package",
      "title": "A method to infer the methylation expression level for each CpG sites.",
      "topics": [
        "SIMD-package"
      ]
    },
    {
      "page": "EMalgorithm",
      "title": "EM algorithm to infer CpG sites.",
      "topics": [
        "EMalgorithm"
      ]
    },
    {
      "page": "emalgth",
      "title": "Calculate the probability on condition that the sums equal to 1.",
      "topics": [
        "emalgth"
      ]
    },
    {
      "page": "emalgth1",
      "title": "Calculate the probability on condition that the sums more than 1.",
      "topics": [
        "emalgth1"
      ]
    },
    {
      "page": "EMtest",
      "title": "Inferring the methylation expression level of single sites.",
      "topics": [
        "EMtest"
      ]
    },
    {
      "page": "probBinom",
      "title": "Compute P-values for Medip-seq and MRE-seq data.",
      "topics": [
        "probBinom"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SIMD/raw/HEAD/README.md",
  "_rundeps": [
    "edgeR",
    "lattice",
    "limma",
    "locfit",
    "methylMnM",
    "statmod"
  ],
  "_vignettes": [
    {
      "source": "SIMD.Rmd",
      "filename": "SIMD.html",
      "title": "SIMD Tutorial",
      "author": "Yan Zhou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1 Introduction",
        "2 Preparations",
        "3 Data format",
        "4 Data Pre-processing",
        "5 p-values of SIMD test",
        "6 Select Significants"
      ],
      "created": "2018-06-29 17:47:54",
      "modified": "2018-08-15 09:06:43",
      "commits": 7
    }
  ],
  "_score": 5,
  "_indexed": true,
  "_nocasepkg": "simd",
  "_universes": [
    "bioc",
    "focuspaka"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-07-04T05:59:42.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/813e99b790a2d0e8c00566ae8e11016d1d9d8bbbef62b801a79f7cf3ac3388ee",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-07-04T06:00:14.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/a75777be192e7cc7ff660b0a84ea4433c905ff01a22edfe95d231410611207a2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-07-04T05:59:27.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/8c2e9c065960834c22fdbb1d72ece16e22db07499b93d55538f3e9c45ba929b2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-07-04T06:00:07.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/64c8d860911ceb2015371dfc9c5df019d9eada10d9d4fb19a858e36ca6bf94f9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-07-04T06:35:55.000Z",
      "arch": "aarch64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/d55d2d21082f1ea1f0593c14d9637f9c1ae5dca9eb5855bf65e11398189738a6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-07-04T05:59:52.000Z",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/ef7cfa83149fcfea2e5a6143b4850d51ad9ce5291b25fa40925695eb19469b9f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-07-04T06:35:13.000Z",
      "arch": "aarch64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/961703945d34a043db9ba8116934a14648e313af1df6971ad55275932334068d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-07-04T06:00:10.000Z",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/117d43192bd59cbafab7e97b362547c69e4d83e91612b9c40c19874510656d1b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.31.0",
      "date": "2026-07-04T05:59:10.000Z",
      "arch": "emscripten",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/dd217f40053133f924a92586642494d23aa3ee54a9f6f93fabe84adba2bc4664",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-07-04T05:58:14.000Z",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/2ae3ce4af6409116c331c6310bc808d69db942d3ae5c71228b101b8c28e080ab",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-07-04T05:58:29.000Z",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/2f1c6f21d53d38941b4c676646337b5c5271ea44e5bfa73dc25b87d7e49040b5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-07-04T05:58:14.000Z",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/a9315a8522486027fe3dfcb66e0bc7890c6f92b60ec32c204e1fb8983df2d57e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28696891481"
    }
  ]
}