{ "_id": "6ad1f51fc96d212026e7032d", "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": "2026-10-16 08:38:43 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "SIMD_1.31.0.tar.gz", "_fileid": "https://r2.ropensci.org/2413122a8c51617e8f87506193340f9d661402730709c06a332f28aa9dd2d68c", "_filesize": 225539, "_sha256": "2413122a8c51617e8f87506193340f9d661402730709c06a332f28aa9dd2d68c", "_expires": "2027-01-24T09:57:49.000Z", "_created": "2026-10-16T08:38:43.000Z", "_published": "2026-10-16T09:57:51.531Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 1, "warning": 0, "note": 11 }, "_upstream": "https://github.com/bioc/SIMD", "_commit": { "id": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "author": "A Wokaty ", "committer": "A Wokaty ", "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": 116888077713, "time": 140, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "12034569865" }, { "job": 116888078039, "time": 98, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "12034514831" }, { "job": 116888078150, "time": 166, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12034449889" }, { "job": 116888077824, "time": 97, "config": "linux-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12035181023" }, { "job": 116888077815, "time": 146, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12035365850" }, { "job": 116888077926, "time": 78, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "12038586557" }, { "job": 116888078018, "time": 162, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "12036126620" }, { "job": 116888077971, "time": 85, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12038951231" }, { "job": 116888077900, "time": 241, "config": "macos-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12036111879" }, { "job": 116886883417, "time": 179, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12035400027" }, { "job": 116888077852, "time": 94, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12034988081" }, { "job": 116888077863, "time": 218, "config": "windows-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "12035226263" }, { "job": 116888077972, "time": 135, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12035241041" }, { "job": 116888077935, "time": 84, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "12034749310" }, { "job": 116888077895, "time": 182, "config": "windows-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12034804554" }, { "job": 116888077985, "time": 82, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12034724448" } ], "_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", "repository": "bioc" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "immunooncology", "differentialmethylation", "singlecell", "differentialexpression" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 477, "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": 2, "_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": "2026-10-16T08:40:20.000Z", "distro": "resolute", "arch": "aarch64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/b112cdb96489bacccbb83cfe9f16c94f2dad8012d16ddd4ef0a523299ec3d322", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-10-16T08:41:32.000Z", "distro": "resolute", "arch": "x86_64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/c276959bd72b5470178e5e8911942ac151041367e9eb3e6b5e18f1478d3c611f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.6.1", "os": "linux", "version": "1.31.0", "date": "2026-10-16T08:40:22.000Z", "distro": "resolute", "arch": "aarch64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/0da044582686b01b64555c494d4971db891a128bf28759c84c3897b79f1b4fba", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.6.1", "os": "linux", "version": "1.31.0", "date": "2026-10-16T08:41:09.000Z", "distro": "resolute", "arch": "x86_64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/22cd8b109195be314a50eaa0690abc9c308170fb2baae4fcd67bf7d05decab49", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", "date": "2026-10-16T09:56:43.000Z", "arch": "aarch64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/6dda7b3714cb31a6f7cacf3f3dfe19a0eab3db4c4f67b8c521f228b465bd1bba", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", "date": "2026-10-16T08:55:51.000Z", "arch": "x86_64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/3782a1445d3187ae8b9b979d7a492599c3e12401e991606b9e4bb0f962356bb9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.6.1", "os": "mac", "version": "1.31.0", "date": "2026-10-16T09:56:54.000Z", "arch": "aarch64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/0b2fdad0ea7aac6f7077a1841525b99cedc989162fefe1c2352c7ac39febbe2e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.6.1", "os": "mac", "version": "1.31.0", "date": "2026-10-16T08:56:38.000Z", "arch": "x86_64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/81022d089f1de86547a48367a25cbf80b2c746a0ecdfa5306f354270b2a1d289", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.6.0", "os": "wasm", "version": "1.31.0", "date": "2026-10-16T08:40:28.000Z", "arch": "emscripten", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/668631758408df4c5c5b7cffca1008764228083d5ebc89c2ef37f34e77d66d2b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.7.0", "os": "win", "version": "1.31.0", "date": "2026-10-16T08:42:12.000Z", "arch": "aarch64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/ead321815104e34191b2588d4cc0e2f5f00ac08629a90f2024f935c035dff8ee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.7.0", "os": "win", "version": "1.31.0", "date": "2026-10-16T08:40:08.000Z", "arch": "x86_64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/7417f0ecc252b8afe535debad296cb92e36c7c29d4cfadfb042cf0711d0d26cc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.5.3", "os": "win", "version": "1.31.0", "date": "2026-10-16T08:39:55.000Z", "arch": "x86_64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/53d5d692d8d2013d5757d8dbb755b0153d976cd3d3fe9f75a7c8e68c7d283182", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.6.1", "os": "win", "version": "1.31.0", "date": "2026-10-16T08:41:37.000Z", "arch": "aarch64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/949e4987347683996ef6036a531f13c4486039d1506d4fbed675d448aea74c4d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" }, { "r": "4.6.1", "os": "win", "version": "1.31.0", "date": "2026-10-16T08:39:57.000Z", "arch": "x86_64", "commit": "3d3c8d543db7b7aec583369916e06ca6a0370cbb", "fileid": "https://r2.ropensci.org/33b8efc72cc449f7acfa283a202747c36b26d6069f6be240d9f2e1b2915b4444", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38874678400" } ] }