{ "_id": "6a339bfc3efcd9bda43a591a", "Package": "POWSC", "Type": "Package", "Title": "Simulation, power evaluation, and sample size recommendation for\nsingle cell RNA-seq", "Version": "1.21.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:56:01 UTC", "RemoteUrl": "https://github.com/bioc/POWSC", "RemoteRef": "HEAD", "RemoteSha": "bc5f0d0a8b74fdec867e009f5cfec7c676033550", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-18 07:09:40 UTC", "User": "root" }, "Author": "Kenong Su [aut, cre],\nHao Wu [aut]", "Maintainer": "Kenong Su ", "MD5sum": "ef1fec10434cfa776ea542f99d64abe3", "_user": "bioc", "_type": "src", "_file": "POWSC_1.21.0.tar.gz", "_fileid": "e4d6a71df3b0e3e5b2c390c6bb865667781ab5464a50e47abd7e7b3a97951154", "_filesize": 1024104, "_sha256": "e4d6a71df3b0e3e5b2c390c6bb865667781ab5464a50e47abd7e7b3a97951154", "_created": "2026-06-18T07:09:40.000Z", "_published": "2026-06-18T07:19:24.424Z", "_jobs": [ { "job": 82074339781, "time": 222, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7716545609" }, { "job": 82074339750, "time": 371, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7716589454" }, { "job": 82074339784, "time": 447, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7716612541" }, { "job": 82074339773, "time": 267, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7716635463" }, { "job": 82074339814, "time": 256, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7716623981" }, 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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": true, "_usedby": 0, "_updates": [ { "week": "2025-42", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_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", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 9, "_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/HEAD/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": true, "_nocasepkg": "powsc", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-06-18T07:13:18.000Z", "distro": "noble", "commit": "bc5f0d0a8b74fdec867e009f5cfec7c676033550", "fileid": "117947f682822221b5bf4735fca43dd8893790127d245097010b05f21735505c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27742710179" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-06-18T07:14:17.000Z", "distro": "noble", "commit": "bc5f0d0a8b74fdec867e009f5cfec7c676033550", "fileid": "387fcbc5a0602c06aff96935535c19794167830cfa8793cb92a8e154a1bc103c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27742710179" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-06-18T07:16:17.000Z", "commit": "bc5f0d0a8b74fdec867e009f5cfec7c676033550", "fileid": "2e07ba0723e63807c140c3fa63aa0dffd921e8105e8a0b9433ed8c4c7ccd8081", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27742710179" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-06-18T07:15:54.000Z", "commit": "bc5f0d0a8b74fdec867e009f5cfec7c676033550", "fileid": "e24d070a7ea565f90e19e4f047146bc33d402a29e50c76def86fb85b2d7624b6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27742710179" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-06-18T07:12:21.000Z", "commit": "bc5f0d0a8b74fdec867e009f5cfec7c676033550", "fileid": "25fb0f1c7dd63008e14d12b59a28a76cfbdaa04e02a6a47eb41d62b2255501be", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27742710179" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-06-18T07:11:50.000Z", "commit": "bc5f0d0a8b74fdec867e009f5cfec7c676033550", "fileid": "9bd5dc500a395cd82699b18ad02b225859e6649563a6c08a732e7c9357eea81a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27742710179" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-06-18T07:11:17.000Z", "commit": "bc5f0d0a8b74fdec867e009f5cfec7c676033550", "fileid": "56703acbf22f3ef5f6049869a7145f716c446b6c17700ef336905322d01e5d6e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27742710179" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-06-18T07:11:25.000Z", "commit": "bc5f0d0a8b74fdec867e009f5cfec7c676033550", "fileid": "cb564078e9eb97ae173105e5b6ec5a2c96053b9e6a023045cd8618e3dc918625", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27742710179" } ] }