{ "_id": "6a49958674ff1be5edd789f2", "Package": "HIREewas", "Type": "Package", "Title": "Detection of cell-type-specific risk-CpG sites in epigenome-wide\nassociation studies", "Version": "1.31.0", "Date": "2018-06-11", "Author": "Xiangyu Luo , Can Yang ,\nYingying Wei ", "Maintainer": "Xiangyu Luo ", "Description": "In epigenome-wide association studies, the measured\nsignals for each sample are a mixture of methylation profiles\nfrom different cell types. The current approaches to the\nassociation detection only claim whether a\ncytosine-phosphate-guanine (CpG) site is associated with the\nphenotype or not, but they cannot determine the cell type in\nwhich the risk-CpG site is affected by the phenotype. We\npropose a solid statistical method, HIgh REsolution (HIRE),\nwhich not only substantially improves the power of association\ndetection at the aggregated level as compared to the existing\nmethods but also enables the detection of risk-CpG sites for\nindividual cell types. The \"HIREewas\" R package is to implement\nHIRE model in R.", "VignetteBuilder": "knitr", "biocViews": "DNAMethylation, DifferentialMethylation, FeatureExtraction", "LazyLoad": "yes", "License": "GPL (>= 2)", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:48:54 UTC", "RemoteUrl": "https://github.com/bioc/HIREewas", "RemoteRef": "HEAD", "RemoteSha": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-04 23:14:39 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "HIREewas_1.31.0.tar.gz", "_fileid": "https://r2.ropensci.org/461f85396c7cf2e1584040ebd1377295c2b5982ee18bdb7edae303d66bad3245", "_filesize": 382925, "_sha256": "461f85396c7cf2e1584040ebd1377295c2b5982ee18bdb7edae303d66bad3245", "_expires": "2026-10-12T23:21:41.000Z", "_created": "2026-07-04T23:14:39.000Z", "_published": "2026-07-04T23:21:42.862Z", "_bioccheck": { "error": 1, "warning": 2, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287", "_status": "success", "_upstream": "https://github.com/bioc/HIREewas", "_commit": { "id": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380534 }, "_maintainer": { "name": "Xiangyu Luo", "email": "xyluo1991@gmail.com", "login": "xiangyuluo", "description": "\n Associate Professor (with tenure), Institute of Statistics and Big Data, Renmin University of China\n", "uuid": 25922838 }, "_distro": "resolute", "_jobs": [ { "job": 85174889310, "time": 153, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8086305966" }, { "job": 85174889329, "time": 166, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8086307605" }, { "job": 85174889344, "time": 179, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8086308615" }, { "job": 85174889349, "time": 175, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8086308540" }, { "job": 85174889350, "time": 183, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8086308946" }, { "job": 85174889328, "time": 88, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8086328195" }, { "job": 85174889333, "time": 190, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "8086311052" }, { "job": 85174889322, "time": 107, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8086330114" }, { "job": 85174889335, "time": 187, "config": "macos-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8086314063" }, { "job": 85174644649, "time": 262, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8086289948" }, { "job": 85174889319, "time": 109, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8086301342" }, { "job": 85174889320, "time": 121, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8086302583" }, { "job": 85174889315, "time": 116, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8086302172" }, { "job": 85174889341, "time": 117, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8086302139" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "quadprog", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocGenerics", "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": [ "dnamethylation", "differentialmethylation", "featureextraction" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 1, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HIREewas.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "HIRE", "riskCpGpattern" ], "_help": [ { "page": "HIREewas-package", "title": "Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies", "topics": [ "HIREewas-package", "HIREewas" ] }, { "page": "HIRE", "title": "Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies", "topics": [ "HIRE" ] }, { "page": "riskCpGpattern", "title": "Plot the detected association pattern with one phenotype using heatmap", "topics": [ "riskCpGpattern" ] } ], "_readme": "https://github.com/bioc/HIREewas/raw/HEAD/README.md", "_rundeps": [ "bitops", "caTools", "gplots", "gtools", "KernSmooth", "quadprog" ], "_vignettes": [ { "source": "HIREewas.Rnw", "filename": "HIREewas.pdf", "title": "HIREewas", "engine": "knitr::knitr", "headings": [ "1 Introduction", "2 Data Preparation", "3 Model Application", "4 Visualization" ], "created": "2018-09-12 07:44:38", "modified": "2018-12-01 04:51:38", "commits": 6 } ], "_score": 4, "_indexed": true, "_nocasepkg": "hireewas", "_universes": [ "bioc", "xiangyuluo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-07-04T23:17:10.000Z", "distro": "resolute", "arch": "aarch64", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/11aba6ca6930aec7a00c3b38e8e25295489e34513c285fe215d02377e308d5f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" }, { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-07-04T23:17:14.000Z", "distro": "resolute", "arch": "x86_64", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/bee9ee56096d7cf6c025f1a0bb3825109bda72ba89d929b975f947a2d47b96e9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" }, { "r": "4.6.1", "os": "linux", "version": "1.31.0", "date": "2026-07-04T23:17:17.000Z", "distro": "resolute", "arch": "aarch64", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/9c5b39bec709e7eea0a46cc450fb65fd673d1cf68b5c203962a52581eb5a250b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" }, { "r": "4.6.1", "os": "linux", "version": "1.31.0", "date": "2026-07-04T23:17:10.000Z", "distro": "resolute", "arch": "x86_64", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/038951043e3660239474966116307c19e2a27442c5456f8dc079f21c725dbc85", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", "date": "2026-07-04T23:20:40.000Z", "arch": "aarch64", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/09c964a2d193fe287ef3092d38e592da71ecfb29f3385f53a249b1d064c648ae", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", "date": "2026-07-04T23:17:24.000Z", "arch": "x86_64", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/b87ea20bf0fc6fcc370ba286dc0665d987fcf46658926e1afe1cbe61ab2961f7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" }, { "r": "4.6.1", "os": "mac", "version": "1.31.0", "date": "2026-07-04T23:20:47.000Z", "arch": "aarch64", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/bfcb1f71d57e2dbd4bbe109ab6605c58c44f2755e8df838a6125d03edafb307c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" }, { "r": "4.6.1", "os": "mac", "version": "1.31.0", "date": "2026-07-04T23:17:55.000Z", "arch": "x86_64", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/986ffb36046c18bef981705ad00688dedb945eff83ae22c851556d2983af3507", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" }, { "r": "4.6.0", "os": "wasm", "version": "1.31.0", "date": "2026-07-04T23:16:43.000Z", "arch": "emscripten", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/7195ae9c22fa7c51ede6330e834b16385758b1fc3b7f2f13ac553f70af2242ae", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" }, { "r": "4.7.0", "os": "win", "version": "1.31.0", "date": "2026-07-04T23:15:48.000Z", "arch": "x86_64", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/d0e91ef89ed8d45ba1163549d1045f4d5b9eab870a03d8e01fdb1b746b1f1380", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" }, { "r": "4.5.3", "os": "win", "version": "1.31.0", "date": "2026-07-04T23:15:46.000Z", "arch": "x86_64", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/9d8800175c89a8aa91b33dfd85f23a53a2bb8ea698aad9a83b63e9e8f1b566ae", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" }, { "r": "4.6.1", "os": "win", "version": "1.31.0", "date": "2026-07-04T23:15:45.000Z", "arch": "x86_64", "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8", "fileid": "https://r2.ropensci.org/365379d0d336ca99c9eb954057e771a76cce63f26c5f08dc0489858ddcc0516d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722650287" } ] }