{ "_id": "6a212494cd65a98ecbd20719", "Package": "SCBN", "Type": "Package", "Title": "A statistical normalization method and differential expression\nanalysis for RNA-seq data between different species", "Version": "1.31.0", "Author": "Yan Zhou", "Maintainer": "Yan Zhou <2160090406@email.szu.edu.cn>", "Description": "This package provides a scale based normalization (SCBN)\nmethod to identify genes with differential expression between\ndifferent species. It takes into account the available\nknowledge of conserved orthologous genes and the hypothesis\ntesting framework to detect differentially expressed\northologous genes. The method on this package are described in\nthe article 'A statistical normalization method and\ndifferential expression analysis for RNA-seq data between\ndifferent species' by Yan Zhou, Jiadi Zhu, Tiejun Tong, Junhui\nWang, Bingqing Lin, Jun Zhang (2018, pending publication).", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "RoxygenNote": "6.0.1", "biocViews": "DifferentialExpression, GeneExpression, Normalization", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:48:28 UTC", "RemoteUrl": "https://github.com/bioc/SCBN", "RemoteRef": "HEAD", "RemoteSha": "6adf75c9d7c92760d0775ed0c7e0a762c986931a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 07:04:54 UTC", "User": "root" }, "MD5sum": "8bd702a076c447aac345eb161a1e29c1", "_user": "bioc", "_type": "src", "_file": "SCBN_1.31.0.tar.gz", "_fileid": "98c3f5ca54478ec8031b353c5c85c32327b96fb4f1b64307320051d1f52fb879", "_filesize": 410771, "_sha256": "98c3f5ca54478ec8031b353c5c85c32327b96fb4f1b64307320051d1f52fb879", "_created": "2026-06-04T07:04:54.000Z", "_published": "2026-06-04T07:09:08.640Z", "_jobs": [ { "job": 79467271233, "time": 136, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7405142250" }, { "job": 79467271278, "time": 227, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7405167383" }, { "job": 79467271300, "time": 189, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7405156954" }, { "job": 79467271244, "time": 168, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7405160173" }, { "job": 79467271241, "time": 161, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7405163999" }, { "job": 79466859376, "time": 179, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7405103844" }, { "job": 79467271221, "time": 90, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7405129016" }, { "job": 79467271321, "time": 202, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7405160458" }, { "job": 79467271257, "time": 218, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7405165242" }, { "job": 79467271271, "time": 195, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7405158382" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26936303500", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/SCBN", "_commit": { "id": "6adf75c9d7c92760d0775ed0c7e0a762c986931a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380508 }, "_maintainer": { "name": "Yan Zhou", "email": "2160090406@email.szu.edu.cn", "login": "focuspaka", "description": "", "uuid": 40629719 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "BiocManager", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_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": [ "differentialexpression", "geneexpression", "normalization" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 307, "source": "https://www.bioconductor.org/packages/stats/bioc/SCBN" }, "_mentions": 2, "_searchresults": 7, "_rbuild": "4.6.0", "_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/SCBN.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "generateDataset", "Iter_optimal", "MediancalcNorm", "sageTestNew", "SCBN" ], "_datasets": [ { "name": "orthgenes", "title": "A real dataset of orthologous genes between the different species.", "object": "orthgenes", "class": [ "data.frame" ], "fields": [ "Ensembl.Gene.ID", "ExonicLength", "Mouse.Ensembl.Gene.ID", "ExonicLength.1", "X..Identity", "Human_Brain_Male1", "Human_Brain_Male2", "Mouse_Brain_Male1", "Mouse_Brain_Male2" ], "rows": 27821, "table": true, "tojson": true }, { "name": "sim_data", "title": "A simulation dataset of orthologous genes between the different species.", "object": "sim_data", "class": [ "data.frame" ], "fields": [ "geneLength1", "counts1", "geneLength2", "counts2" ], "rows": 4143, "table": true, "tojson": true } ], "_help": [ { "page": "generateDataset", "title": "Generate simulation data for different species", "topics": [ "generateDataset" ] }, { "page": "To", "title": "Iteration to find the optimal value A iteration process to compute the normalization factor to identify difference expression(DE) of genes between different species", "topics": [ "Iter_optimal", "MediancalcNorm", "sageTestNew" ] }, { "page": "orthgene", "title": "A real dataset of orthologous genes between the different species.", "topics": [ "orthgenes" ] }, { "page": "SCBN", "title": "Compute the normalization factor to identify difference expression (DE) of genes between different species", "topics": [ "SCBN" ] }, { "page": "sim_data", "title": "A simulation dataset of orthologous genes between the different species.", "topics": [ "sim_data" ] } ], "_readme": "https://github.com/bioc/SCBN/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "SCBN.Rmd", "filename": "SCBN.html", "title": "SCBN Tutorial", "author": "Yan Zhou", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Preparations", "Data format", "Calculate scaling factor for data", "Calculate p-values for each orthologous genes and select significants" ], "created": "2018-08-16 14:52:57", "modified": "2023-04-17 16:23:25", "commits": 3 } ], "_score": 4.778151250383644, "_indexed": true, "_nocasepkg": "scbn", "_universes": [ "bioc", "focuspaka" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-06-04T07:07:49.000Z", "distro": "noble", "commit": "6adf75c9d7c92760d0775ed0c7e0a762c986931a", "fileid": "194ca8766580b27f7161ffd1799eeeaa5a9d0f4a58a308f9bb977199ac13951f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26936303500" }, { "r": "4.6.0", "os": "linux", "version": "1.31.0", "date": "2026-06-04T07:07:10.000Z", "distro": "noble", "commit": "6adf75c9d7c92760d0775ed0c7e0a762c986931a", "fileid": "6562ebf99f3f0ad3b47ea9794ead0f6f13a751d1761500b4585529eec125c4d3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26936303500" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", "date": "2026-06-04T07:07:27.000Z", "commit": "6adf75c9d7c92760d0775ed0c7e0a762c986931a", "fileid": "934c8a689a3993f118a07ce148e32766eb24e4ab7ff695e23311bb52753fcefc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26936303500" }, { "r": "4.6.0", "os": "mac", "version": "1.31.0", "date": "2026-06-04T07:07:48.000Z", "commit": "6adf75c9d7c92760d0775ed0c7e0a762c986931a", "fileid": "e7058b47a644e64130e56d2e45deb65b88dcbb205757b2b60b0d81a789a236dd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26936303500" }, { "r": "4.6.0", "os": "wasm", "version": "1.31.0", "date": "2026-06-04T07:06:37.000Z", "commit": "6adf75c9d7c92760d0775ed0c7e0a762c986931a", "fileid": "fe8961fcb480fd50c8faf4aa4a380dd826d22e72a2930473ff947fbacbc32f86", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26936303500" }, { "r": "4.7.0", "os": "win", "version": "1.31.0", "date": "2026-06-04T07:06:32.000Z", "commit": "6adf75c9d7c92760d0775ed0c7e0a762c986931a", "fileid": "61521b9b5241c27c4923b27bcd44e58039dd61b9c16f7164635fb67a4d6b8e9f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26936303500" }, { "r": "4.5.3", "os": "win", "version": "1.31.0", "date": "2026-06-04T07:07:02.000Z", "commit": "6adf75c9d7c92760d0775ed0c7e0a762c986931a", "fileid": "9d1863ec6aca41efb9ebf17c06a44eea7ed57a853f81900a49c7c4e9b398631c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26936303500" }, { "r": "4.6.0", "os": "win", "version": "1.31.0", "date": "2026-06-04T07:06:04.000Z", "commit": "6adf75c9d7c92760d0775ed0c7e0a762c986931a", "fileid": "8ffe48f7f7548ae9421e8cf2e69ff16bbe61457b7c425edf857649f98d0db4b5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26936303500" } ] }