{ "_id": "6a27af3624555f66ed53509b", "Package": "SimSeq", "Type": "Package", "Title": "Nonparametric Simulation of RNA-Seq Data", "Version": "1.4.0", "Date": "2015-11-22", "Author": "Samuel Benidt", "Maintainer": "Samuel Benidt ", "Description": "RNA sequencing analysis methods are often derived by\nrelying on hypothetical parametric models for read counts that\nare not likely to be precisely satisfied in practice. Methods\nare often tested by analyzing data that have been simulated\naccording to the assumed model. This testing strategy can\nresult in an overly optimistic view of the performance of an\nRNA-seq analysis method. We develop a data-based simulation\nalgorithm for RNA-seq data. The vector of read counts simulated\nfor a given experimental unit has a joint distribution that\nclosely matches the distribution of a source RNA-seq dataset\nprovided by the user. Users control the proportion of genes\nsimulated to be differentially expressed (DE) and can provide a\nvector of weights to control the distribution of effect sizes.\nThe algorithm requires a matrix of RNA-seq read counts with\nlarge sample sizes in at least two treatment groups. Many\ndatasets are available that fit this standard.", "License": "GPL (>= 2)", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-08 08:11:34 UTC", "User": "root" }, "Repository": "https://sbenidt.r-universe.dev", "Date/Publication": "2015-11-23 12:33:58 UTC", "RemoteUrl": "https://github.com/cran/SimSeq", "RemoteRef": "HEAD", "RemoteSha": "256a72d0b3cd24ff68541624ce35a6e9182cf450", "MD5sum": "6058f70da2612d6036f1d47b2abccc3f", "_user": "sbenidt", "_type": "src", "_file": "SimSeq_1.4.0.tar.gz", "_fileid": "e1e85c6ad599ae72e58e6d507b439c363bee4ed8a1067fc00051901f13c1ccc9", "_filesize": 4531346, "_sha256": "e1e85c6ad599ae72e58e6d507b439c363bee4ed8a1067fc00051901f13c1ccc9", "_created": "2026-06-08T08:11:34.000Z", "_published": "2026-06-09T06:14:14.112Z", "_distro": "noble", "_jobs": [ { "job": 80256828421, "time": 102, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7474751088" }, { "job": 80256828583, "time": 98, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7474750124" }, { "job": 80256828098, "time": 126, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7499854904" }, { "job": 80256828137, "time": 165, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7499827477" }, { "job": 80256828171, "time": 227, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7474716940" }, { "job": 80256828561, "time": 88, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7474746934" }, { "job": 80256828333, "time": 77, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7474742950" }, { "job": 80256828668, "time": 160, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7474770055" }, { "job": 80256828537, "time": 171, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7474774245" } ], "_buildurl": "https://github.com/r-universe/sbenidt/actions/runs/27124364878", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/SimSeq", "_commit": { "id": "256a72d0b3cd24ff68541624ce35a6e9182cf450", "author": "Samuel Benidt ", "committer": "Gabor Csardi ", "message": "version 1.4.0\n", "time": 1448282038 }, "_maintainer": { "name": "Samuel Benidt", "email": "sgbenidt@gmail.com", "login": "sbenidt", "uuid": 2745653 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10.0", "role": "Depends" }, { "package": "fdrtool", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "sbenidt", "count": 4, "uuid": 2745653 } ], "_userbio": { "uuid": 2745653, "type": "user", "name": "Samuel Benidt" }, "_downloads": { "count": 147, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SimSeq" }, "_mentions": 36, "_searchresults": 18, "_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/SimSeq.html", "manual.pdf" ], "_realowner": "sbenidt", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2014-02-18" }, { "version": "1.2.0", "date": "2014-12-10" }, { "version": "1.3.0", "date": "2015-03-07" }, { "version": "1.4.0", "date": "2015-11-23" } ], "_exports": [ "CalcPvalWilcox", "SimData", "SortData" ], "_datasets": [ { "name": "kidney", "title": "Kidney Renal Clear Cell Carcinoma [KIRC] RNA-Seq data", "object": "kidney", "file": "kidney.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "SimSeq-package", "title": "Nonparametric Simulation of RNA-Seq Data", "topics": [ "SimSeq-package", "SimSeq" ] }, { "page": "CalcPvalWilcox", "title": "Calculate P-values of Differential Expression", "topics": [ "CalcPvalWilcox" ] }, { "page": "kidney", "title": "Kidney Renal Clear Cell Carcinoma [KIRC] RNA-Seq data", "topics": [ "kidney" ] }, { "page": "SimData", "title": "SimData", "topics": [ "SimData" ] }, { "page": "SortData", "title": "SortData", "topics": [ "SortData" ] } ], "_rundeps": [ "fdrtool" ], "_score": 2.255272505103306, "_indexed": true, "_nocasepkg": "simseq", "_universes": [ "sbenidt" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.0", "date": "2026-06-08T08:14:11.000Z", "distro": "noble", "commit": "256a72d0b3cd24ff68541624ce35a6e9182cf450", "fileid": "52b2cceb3221bdb04b4575b1626b00266a17c1a802bd832abefbd166fa164b2b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sbenidt/actions/runs/27124364878" }, { "r": "4.6.0", "os": "linux", "version": "1.4.0", "date": "2026-06-08T08:14:08.000Z", "distro": "noble", "commit": "256a72d0b3cd24ff68541624ce35a6e9182cf450", "fileid": "8b0c5bd0059aafafe5484a830eb83c69e4fd4998367b51635e6e598ce1cd59b5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sbenidt/actions/runs/27124364878" }, { "r": "4.5.3", "os": "mac", "version": "1.4.0", "date": "2026-06-09T06:13:32.000Z", "commit": "256a72d0b3cd24ff68541624ce35a6e9182cf450", "fileid": "e4727eb3fcad45ddc59476150e0760d873e2807623d63d0e4c3f9eb32f81a62d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sbenidt/actions/runs/27124364878" }, { "r": "4.6.0", "os": "mac", "version": "1.4.0", "date": "2026-06-09T06:11:42.000Z", "commit": "256a72d0b3cd24ff68541624ce35a6e9182cf450", "fileid": "d8fa5c92d140ead7b7d30eb31e071e16f9912221ac8795f90b989e15baf42b3c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sbenidt/actions/runs/27124364878" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.0", "date": "2026-06-08T08:14:10.000Z", "commit": "256a72d0b3cd24ff68541624ce35a6e9182cf450", "fileid": "936f87a583b8ec0be12fd95f78e35db2cd7aaf3ef98e3d2198846cd563b940bc", "status": "success", "buildurl": "https://github.com/r-universe/sbenidt/actions/runs/27124364878" }, { "r": "4.7.0", "os": "win", "version": "1.4.0", "date": "2026-06-08T08:13:41.000Z", "commit": "256a72d0b3cd24ff68541624ce35a6e9182cf450", "fileid": "bf2e8ea8f5b636bf54b4771d4b899d79c05869ae1b4cdcd2ff829002a12ac28d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sbenidt/actions/runs/27124364878" }, { "r": "4.5.3", "os": "win", "version": "1.4.0", "date": "2026-06-08T08:15:02.000Z", "commit": "256a72d0b3cd24ff68541624ce35a6e9182cf450", "fileid": "baf4402dc556d833fe049f806d3e8b01994ce9e0c563d326f379139c3f91fd6d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sbenidt/actions/runs/27124364878" }, { "r": "4.6.0", "os": "win", "version": "1.4.0", "date": "2026-06-08T08:15:11.000Z", "commit": "256a72d0b3cd24ff68541624ce35a6e9182cf450", "fileid": "afac54a5e249bf69ff8337a57ee6d5037620325c60aa931d83921a2cc9b3316b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sbenidt/actions/runs/27124364878" } ] }