{
  "_id": "6aaa611dea78b3e62eacbc50",
  "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": "2026-09-16 09:21:54 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "SIMD_1.31.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/88e8ab275823d37fb7464e9b175b384bc3aa28ca8d7cd2f3e014ac9de0064492",
  "_filesize": 225867,
  "_sha256": "88e8ab275823d37fb7464e9b175b384bc3aa28ca8d7cd2f3e014ac9de0064492",
  "_expires": "2026-12-25T09:27:55.000Z",
  "_created": "2026-09-16T09:21:54.000Z",
  "_published": "2026-09-16T09:27:57.007Z",
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 11
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262",
  "_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": 104738233370,
      "time": 139,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "10439471518"
    },
    {
      "job": 104738233401,
      "time": 118,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10439581088"
    },
    {
      "job": 104738233501,
      "time": 163,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10439447755"
    },
    {
      "job": 104738233484,
      "time": 146,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10439522533"
    },
    {
      "job": 104738233376,
      "time": 188,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10439681665"
    },
    {
      "job": 104738233534,
      "time": 96,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10439486448"
    },
    {
      "job": 104738233550,
      "time": 223,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10439363526"
    },
    {
      "job": 104738233535,
      "time": 96,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10439283460"
    },
    {
      "job": 104738233439,
      "time": 321,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10439134720"
    },
    {
      "job": 104737299911,
      "time": 172,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10438969115"
    },
    {
      "job": 104738233399,
      "time": 123,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10439541219"
    },
    {
      "job": 104738233548,
      "time": 205,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10439826015"
    },
    {
      "job": 104738233576,
      "time": 106,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10439012897"
    },
    {
      "job": 104738233559,
      "time": 67,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10438934419"
    },
    {
      "job": 104738233582,
      "time": 189,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10439766276"
    },
    {
      "job": 104738233498,
      "time": 68,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10439875151"
    }
  ],
  "_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": 467,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 373,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SIMD"
  },
  "_mentions": 83,
  "_searchresults": 4,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SIMD.html"
  ],
  "_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": "2026-09-16T09:24:01.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/6f1ffa2ed90a7611003d85117b15b340c4db3f686ee19260518d4c9f97994c67",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-09-16T09:24:40.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/28f3e07c281e63701710f9a61826656ba39d0f283433e7830bade6d967ff5d9b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-09-16T09:24:30.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/dc4f989bd996bcf4c73c71731fdcb6ba163806027b7727717e94bdf95f6b63e9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-09-16T09:25:09.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/d3775d007b5970b8fcef329ccba49f411fd721681263fcb21570ace645edd503",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-09-16T09:23:40.000Z",
      "arch": "aarch64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/229dd728a8e31c45ba9a1e64d2c0bbdf3706681d479eac2e127c8b1c3809dc1f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-09-16T09:25:28.000Z",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/0786f6c9f1e61672d8d12756caf9fb77db11046493e2873c03a12b248c3de55a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-09-16T09:23:37.000Z",
      "arch": "aarch64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/f60c9f075afb1ac94106651ade7d2971dc0ecc3d6974ddbbd316fda5ed31adb6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-09-16T09:26:53.000Z",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/aeb3f2bc1009f5a64917fd4955fdf6c2c655bc72ddbacce6dea0ce8a2e57b10d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.31.0",
      "date": "2026-09-16T09:24:15.000Z",
      "arch": "emscripten",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/a2bdf5dee96608f991f664dc06ffc854be372c6a457610ed46c19b6842ddaa83",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-09-16T09:25:13.000Z",
      "arch": "aarch64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/120612d560869a7e06a18e177e401fa2e37ed1ca472df7aa4dbbfa74ded081a8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-09-16T09:22:59.000Z",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/45a255542f27f49ceddbbd8c89b5e5c2913d26b79bbef99335a299cadc312243",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-09-16T09:23:02.000Z",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/e8f14f59a08a8b564bada3362e30422413344c9f5c56c54b8cfb4320126534fe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-09-16T09:25:01.000Z",
      "arch": "aarch64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/0d9df913495f7e7d8810e8d07b0c05eec96333a588a1523b0bfdf3cbb3c02ad8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-09-16T09:22:59.000Z",
      "arch": "x86_64",
      "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb",
      "fileid": "https://r2.ropensci.org/8c5cbc92793847f6fecfa5249ac9472ab3c9b5317fd80b44b476c12d0a8170f3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35078690262"
    }
  ]
}