{
  "_id": "6a1d4b781d7bb097a0a438ea",
  "Package": "ssizeRNA",
  "Type": "Package",
  "Title": "Sample Size Calculation for RNA-Seq Experimental Design",
  "Version": "1.3.3",
  "Date": "2025-04-08",
  "Authors@R": "c(\nperson(\"Ran\", \"Bi\", email = \"biranpier@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Peng\", \"Liu\", email = \"pliu@iastate.edu\", role = \"aut\"),\nperson(\"Tim\", \"Triche\", email = \"tim.triche@gmail.com\", role = \"ctb\"))",
  "Maintainer": "Ran Bi <biranpier@gmail.com>",
  "Description": "We propose a procedure for sample size calculation while\ncontrolling false discovery rate for RNA-seq experimental\ndesign. Our procedure depends on the Voom method proposed for\nRNA-seq data analysis by Law et al. (2014)\n<DOI:10.1186/gb-2014-15-2-r29> and the sample size calculation\nmethod proposed for microarray experiments by Liu and Hwang\n(2007) <DOI:10.1093/bioinformatics/btl664>. We develop a set of\nfunctions that calculates appropriate sample sizes for\ntwo-sample t-test for RNA-seq experiments with fixed or varied\nset of parameters. The outputs also contain a plot of power\nversus sample size, a table of power at different sample sizes,\nand a table of critical test values at different sample sizes.\nTo install this package, please use\n'source(\"http://bioconductor.org/biocLite.R\");\nbiocLite(\"ssizeRNA\")'. For R version 3.5 or greater, please use\n'if(!requireNamespace(\"BiocManager\", quietly =\nTRUE)){install.packages(\"BiocManager\")};\nBiocManager::install(\"ssizeRNA\")'.",
  "VignetteBuilder": "knitr",
  "License": "GPL (>= 2)",
  "biocViews": "GeneExpression, DifferentialExpression, ExperimentalDesign,\nSequencing, RNASeq, DNASeq, Microarray",
  "RoxygenNote": "6.1.1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-01 09:01:59 UTC",
    "User": "root"
  },
  "Author": "Ran Bi [aut, cre], Peng Liu [aut], Tim Triche [ctb]",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://ranbi1990.r-universe.dev",
  "Date/Publication": "2025-04-08 23:30:03 UTC",
  "RemoteUrl": "https://github.com/cran/ssizeRNA",
  "RemoteRef": "HEAD",
  "RemoteSha": "fab65408eee42fc2f3bee1470f25b55cf91aa522",
  "MD5sum": "daaf73ce589f7d499b2372307f5e98ec",
  "_user": "ranbi1990",
  "_type": "src",
  "_file": "ssizeRNA_1.3.3.tar.gz",
  "_fileid": "fe03efb65de230ce0280d294db5e1377e33a391f89051520c717a4244a888d25",
  "_filesize": 540072,
  "_sha256": "fe03efb65de230ce0280d294db5e1377e33a391f89051520c717a4244a888d25",
  "_created": "2026-06-01T09:01:59.000Z",
  "_published": "2026-06-01T09:06:00.447Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78819559752,
      "time": 148,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7327471124"
    },
    {
      "job": 78819559784,
      "time": 147,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7327470767"
    },
    {
      "job": 78819559791,
      "time": 200,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7327478256"
    },
    {
      "job": 78819559757,
      "time": 196,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7327475325"
    },
    {
      "job": 78818948500,
      "time": 220,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7327421082"
    },
    {
      "job": 78819559748,
      "time": 117,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7327460563"
    },
    {
      "job": 78819559779,
      "time": 120,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7327461721"
    },
    {
      "job": 78819559780,
      "time": 106,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7327457182"
    },
    {
      "job": 78819559824,
      "time": 113,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7327459505"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ranbi1990/actions/runs/26745225970",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/ssizeRNA",
  "_commit": {
    "id": "fab65408eee42fc2f3bee1470f25b55cf91aa522",
    "author": "Ran Bi <biranpier@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.3.3\n",
    "time": 1744155003
  },
  "_maintainer": {
    "name": "Ran Bi",
    "email": "biranpier@gmail.com",
    "login": "ranbi1990",
    "description": "",
    "uuid": 176956695
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.2.3",
      "role": "Depends"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "qvalue",
      "role": "Imports"
    },
    {
      "package": "ssize.fdr",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "geneexpression",
    "differentialexpression",
    "experimentaldesign",
    "sequencing",
    "rnaseq",
    "dnaseq",
    "microarray"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "biran1990",
      "count": 6,
      "uuid": 11745228
    },
    {
      "user": "ranbi1990",
      "count": 3,
      "uuid": 176956695
    }
  ],
  "_userbio": {
    "uuid": 176956695,
    "type": "user",
    "name": "ranbi1990"
  },
  "_downloads": {
    "count": 295,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ssizeRNA"
  },
  "_mentions": 4,
  "_searchresults": 42,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/ssizeRNA.html",
    "manual.pdf"
  ],
  "_realowner": "ranbi1990",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.1.1",
      "date": "2015-04-29"
    },
    {
      "version": "1.1.2",
      "date": "2015-05-12"
    },
    {
      "version": "1.2.4",
      "date": "2016-02-11"
    },
    {
      "version": "1.2.6",
      "date": "2016-07-15"
    },
    {
      "version": "1.2.8",
      "date": "2016-10-22"
    },
    {
      "version": "1.2.9",
      "date": "2017-01-09"
    },
    {
      "version": "1.3.1",
      "date": "2019-02-19"
    },
    {
      "version": "1.3.2",
      "date": "2019-08-20"
    },
    {
      "version": "1.3.3",
      "date": "2025-04-08"
    }
  ],
  "_exports": [
    "check.power",
    "sim.counts",
    "ssize.twoSampVaryDelta",
    "ssizeRNA_single",
    "ssizeRNA_vary"
  ],
  "_datasets": [
    {
      "name": "hammer.eset",
      "title": "RNA-seq data from Hammer, P. et al., 2010",
      "object": "hammer.eset",
      "file": "hammer.eset.RData",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "check.power",
      "title": "Average Power and True FDR Based on limma/voom RNAseq Analysis Pipeline",
      "topics": [
        "check.power"
      ]
    },
    {
      "page": "hammer.eset",
      "title": "RNA-seq data from Hammer, P. et al., 2010",
      "topics": [
        "hammer.eset"
      ]
    },
    {
      "page": "sim.counts",
      "title": "RNA-seq Count Data Simulation from Negative-Binomial Distribution",
      "topics": [
        "sim.counts"
      ]
    },
    {
      "page": "ssize.twoSampVaryDelta",
      "title": "Sample Size Calculations for Two-Sample Microarray Experiments with Differing Mean Expressions but fixed Standard Deviations Among Genes",
      "topics": [
        "ssize.twoSampVaryDelta"
      ]
    },
    {
      "page": "ssizeRNA_single",
      "title": "Sample Size Calculations for Two-Sample RNA-seq Experiments with Single Set of Parameters",
      "topics": [
        "ssizeRNA_single"
      ]
    },
    {
      "page": "ssizeRNA_vary",
      "title": "Sample Size Calculations for Two-Sample RNA-seq Experiments with Differing Mean and Dispersion Among Genes",
      "topics": [
        "ssizeRNA_vary"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "cli",
    "cpp11",
    "edgeR",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "plyr",
    "qvalue",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "S7",
    "scales",
    "ssize.fdr",
    "statmod",
    "stringi",
    "stringr",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "ssizeRNA.Rnw",
      "filename": "ssizeRNA.pdf",
      "title": "Sample Size Calculation for RNA-Seq Experimental Design",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2016-02-12 00:57:42",
      "modified": "2017-01-09 09:00:34",
      "commits": 4
    }
  ],
  "_score": 3.7024305364455254,
  "_indexed": true,
  "_nocasepkg": "ssizerna",
  "_universes": [
    "ranbi1990"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.3",
      "date": "2026-06-01T09:04:06.000Z",
      "distro": "noble",
      "commit": "fab65408eee42fc2f3bee1470f25b55cf91aa522",
      "fileid": "8d6cbea945c552abf65090bbc40432109e6cc8cf6437c1b5bc8fc48c721ff5af",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ranbi1990/actions/runs/26745225970"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.3",
      "date": "2026-06-01T09:04:05.000Z",
      "distro": "noble",
      "commit": "fab65408eee42fc2f3bee1470f25b55cf91aa522",
      "fileid": "b1a77f8d4d3736578ac50a733b82508803038259415bc2c2e9c70ccce63bcb87",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ranbi1990/actions/runs/26745225970"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.3",
      "date": "2026-06-01T09:04:36.000Z",
      "commit": "fab65408eee42fc2f3bee1470f25b55cf91aa522",
      "fileid": "6b18b23b5a62def32655de1833c50654ad71ef711de3940558725fba0e47e858",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ranbi1990/actions/runs/26745225970"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.3.3",
      "date": "2026-06-01T09:04:20.000Z",
      "commit": "fab65408eee42fc2f3bee1470f25b55cf91aa522",
      "fileid": "6776e2c9c5edf10fb602cecce48bfdea9cb260237b90fdeea706b38134af1bad",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ranbi1990/actions/runs/26745225970"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.3",
      "date": "2026-06-01T09:04:16.000Z",
      "commit": "fab65408eee42fc2f3bee1470f25b55cf91aa522",
      "fileid": "763b297f3023c53e842977030ef0921c550b8b7f1cfd25b14f841c16dcbfedb2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ranbi1990/actions/runs/26745225970"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.3",
      "date": "2026-06-01T09:03:30.000Z",
      "commit": "fab65408eee42fc2f3bee1470f25b55cf91aa522",
      "fileid": "f53de1a69eea9f06b2c991602138711689d537ff1bca02e6debdda15fd56c1c6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ranbi1990/actions/runs/26745225970"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3.3",
      "date": "2026-06-01T09:03:14.000Z",
      "commit": "fab65408eee42fc2f3bee1470f25b55cf91aa522",
      "fileid": "6abca2e5623e37e2f54f4e098cd77e2c214efa736ac82e2708a6bb107e17f68e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ranbi1990/actions/runs/26745225970"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.3.3",
      "date": "2026-06-01T09:03:17.000Z",
      "commit": "fab65408eee42fc2f3bee1470f25b55cf91aa522",
      "fileid": "d15d345eadefd284bd3557fdf7e95df822eedc1a89f37f2d1cb3bcee226a511b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ranbi1990/actions/runs/26745225970"
    }
  ]
}