{ "_id": "6a194fbcacfb0bcc41ddf160", "Package": "POWSC", "Type": "Package", "Title": "Simulation, power evaluation, and sample size recommendation for\nsingle cell RNA-seq", "Version": "1.20.0", "Authors@R": "c(person(\"Kenong\",\"Su\", email =\"kenong.su@emory.edu\", role = c(\"aut\",\"cre\")),person(\"Hao\",\"Wu\", email =\"hao.wu@emory.edu\", role =\"aut\"))", "Description": "Determining the sample size for adequate power to detect\nstatistical significance is a crucial step at the design stage\nfor high-throughput experiments. Even though a number of\nmethods and tools are available for sample size calculation for\nmicroarray and RNA-seq in the context of differential\nexpression (DE), this topic in the field of single-cell RNA\nsequencing is understudied. Moreover, the unique data\ncharacteristics present in scRNA-seq such as sparsity and\nheterogeneity increase the challenge. We propose POWSC, a\nsimulation-based method, to provide power evaluation and sample\nsize recommendation for single-cell RNA sequencing DE analysis.\nPOWSC consists of a data simulator that creates realistic\nexpression data, and a power assessor that provides a\ncomprehensive evaluation and visualization of the power and\nsample size relationship.", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "biocViews": "DifferentialExpression, ImmunoOncology, SingleCell, Software", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.1", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:56:01 UTC", "RemoteUrl": "https://github.com/bioc/POWSC", "RemoteRef": "RELEASE_3_23", "RemoteSha": "00943d07bf85020cdd5d814c2707d72efe315be9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:26:51 UTC", "User": "root" }, "Author": "Kenong Su [aut, cre],\nHao Wu [aut]", "Maintainer": "Kenong Su ", "MD5sum": "1a5f31b16bfacbed965d2506c75ad4ca", "_user": "bioc-release", "_type": "src", "_file": "POWSC_1.20.0.tar.gz", "_fileid": "a9e5a6b5097b0f9ab317c0140e41c3b19349a461e289881aa5a5d73736ad025d", "_filesize": 1022550, "_sha256": "a9e5a6b5097b0f9ab317c0140e41c3b19349a461e289881aa5a5d73736ad025d", "_created": "2026-05-29T07:26:51.000Z", "_published": "2026-05-29T08:35:08.268Z", "_jobs": [ { "job": 78457061117, "time": 178, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7285428601" }, { "job": 78457061110, "time": 337, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7285476347" }, { "job": 78457061104, "time": 355, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7285481188" }, { "job": 78457061138, "time": 239, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7286537597" }, { "job": 78457061125, "time": 181, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", 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version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380961 }, "_maintainer": { "name": "Kenong Su", "email": "kenong.su@emory.edu" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "SingleCellExperiment", "role": "Depends" }, { "package": "MAST", "role": "Depends" }, { "package": "pheatmap", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-42", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "differentialexpression", "immunooncology", "singlecell", "software" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 284, "source": "https://www.bioconductor.org/packages/stats/bioc/POWSC" }, "_searchresults": 10, "_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/POWSC.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "Est2Phase", "plot_POWSC", "Power_Cont", "Power_Disc", "runDE", "runPOWSC", "Simulate2SCE", "SimulateMultiSCEs", "summary_POWSC" ], "_datasets": [ { "name": "es_mef_sce", "title": "sample data for POWSC", "object": "es_mef_sce", "class": [ "SingleCellExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "sce", "title": "sample data for GSE67835", "object": "GSE67835_AB_S7_sce", "class": [ "SingleCellExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "es_mef_sce", "title": "sample data for POWSC", "topics": [ "es_mef_sce" ] }, { "page": "Est2Phase", "title": "Estimate characterized parameters for a given scRNA-seq data (SingleCellExperiment object or a count matrix).", "topics": [ "Est2Phase" ] }, { "page": "plot_POWSC", "title": "plot the result use visualization.", "topics": [ "plot_POWSC" ] }, { "page": "Power_Cont", "title": "Run DE analysis by using MAST. Here we output two result tables corresponding to two forms of DE genes. These parameters include four gene-wise parameters and two cell-wise parameters.", "topics": [ "Power_Cont" ] }, { "page": "Power_Disc", "title": "Run DE analysis by using MAST. Here we output two result tables corresponding to two forms of DE genes. These parameters include four gene-wise parameters and two cell-wise parameters.", "topics": [ "Power_Disc" ] }, { "page": "runDE", "title": "A wrapper function for calling DE genes. This contains two methods: MAST and SC2P", "topics": [ "runDE" ] }, { "page": "runMAST", "title": "Run DE analysis by using MAST. Here we output two result tables corresponding to two forms of DE genes. These parameters include four gene-wise parameters and two cell-wise parameters.", "topics": [ "runMAST" ] }, { "page": "runPOWSC", "title": "Estimate characterized parameters for a given scRNA-seq data (SingleCellExperiment object or a count matrix).", "topics": [ "runPOWSC" ] }, { "page": "runSC2P", "title": "Run DE analysis by using SC2P. Here we output two result tables corresponding to two forms of DE genes.", "topics": [ "runSC2P" ] }, { "page": "sce", "title": "sample data for GSE67835", "topics": [ "sce" ] }, { "page": "Simulate2SCE", "title": "Simulate the data for two-group comparison; e.g., treatment v.s. control It simulates the DE changes in two forms corresponding two types of DE genes", "topics": [ "Simulate2SCE" ] }, { "page": "SimulateMultiSCEs", "title": "Simulate the data for multiple-group comparisons; e.g., different cell types in blood It simulates the DE changes in two forms corresponding two types of DE genes", "topics": [ "SimulateMultiSCEs" ] }, { "page": "summary_POWSC", "title": "summary of the result", "topics": [ "summary_POWSC" ] } ], "_readme": "https://github.com/bioc/POWSC/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "cpp11", "crayon", "data.table", "DelayedArray", "farver", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "hms", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "limma", "magrittr", "MAST", "Matrix", "MatrixGenerics", "matrixStats", "pheatmap", "pkgconfig", "plyr", "prettyunits", "progress", "R6", "RColorBrewer", "Rcpp", "reshape2", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SingleCellExperiment", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "POWSC.Rmd", "filename": "POWSC.html", "title": "POWSC: power and sample size snalysis for single-cell RNA-seq", "author": "Kenong Su @Emory, Zhijin Wu @Brown, Hao Wu @Emory", "engine": "knitr::rmarkdown", "headings": [ "Installation and quick start", "Installation", "Quick start on using POWSC", "Background", "Introduction", "Use POWSC", "For two-group comparison", "For multiple-group comparisons", "Session Info" ], "created": "2021-03-19 16:38:09", "modified": "2021-05-01 07:38:36", "commits": 4 } ], "_score": 4.176091259055681, "_indexed": false, "_nocasepkg": "powsc", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/POWSC", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-05-29T07:29:55.000Z", "distro": "noble", "commit": "00943d07bf85020cdd5d814c2707d72efe315be9", "fileid": "2866ad1645c864e11926da3b86c9e3167b5ce654ddf52096bd721882f3a18c25", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624036635" }, { "r": "4.6.0", "os": "linux", "version": "1.20.0", "date": "2026-05-29T07:29:47.000Z", "distro": "noble", "commit": "00943d07bf85020cdd5d814c2707d72efe315be9", "fileid": "0d05079ff1bb96df7ec6d78b2dc33fcba4135a32c01e0dfdbc5f91fa9af028ec", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624036635" }, { "r": "4.5.3", "os": "mac", "version": "1.20.0", "date": "2026-05-29T08:32:16.000Z", "commit": "00943d07bf85020cdd5d814c2707d72efe315be9", "fileid": "c669b7b46728c91b0481dc6a7326964092d4bb7329a0b8d7e920623de9eec7ca", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624036635" }, { "r": "4.6.0", "os": "mac", "version": "1.20.0", "date": "2026-05-29T08:31:45.000Z", "commit": "00943d07bf85020cdd5d814c2707d72efe315be9", "fileid": "1d34d46d4d8035d7a462433736861ddc69074011d3dabad9803ea88fa5febca4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624036635" }, { "r": "4.6.0", "os": "wasm", "version": "1.20.0", "date": "2026-05-29T07:29:23.000Z", "commit": "00943d07bf85020cdd5d814c2707d72efe315be9", "fileid": "adc5bdb9dbba5d3295c15867218d601cd8ff69c8850beb09332eb2165f32fc52", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624036635" }, { "r": "4.7.0", "os": "win", "version": "1.20.0", "date": "2026-05-29T07:28:29.000Z", "commit": "00943d07bf85020cdd5d814c2707d72efe315be9", "fileid": "61cbb20adcbb5804e133b207b62950ca968b64a4e21d2dc300dc699dd6e3325d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624036635" }, { "r": "4.5.3", "os": "win", "version": "1.20.0", "date": "2026-05-29T07:29:16.000Z", "commit": "00943d07bf85020cdd5d814c2707d72efe315be9", "fileid": "b620b5b79d44e23fd9e6810c02b5c4e9c22441e90dfdda582d29435662cb633b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624036635" }, { "r": "4.6.0", "os": "win", "version": "1.20.0", "date": "2026-05-29T07:28:52.000Z", "commit": "00943d07bf85020cdd5d814c2707d72efe315be9", "fileid": "b209659d3fdf3540bd1e10dc62e88770d88e81ec4f31aa0016057c16b09cd5b9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624036635" } ] }