{ "_id": "6a194ef7acfb0bcc41dded9f", "Package": "PROPER", "Type": "Package", "Title": "PROspective Power Evaluation for RNAseq", "Version": "1.44.0", "Date": "2020-11-25", "Author": "Hao Wu", "Maintainer": "Hao Wu ", "Description": "This package provide simulation based methods for\nevaluating the statistical power in differential expression\nanalysis from RNA-seq data.", "License": "GPL", "biocViews": "ImmunoOncology, Sequencing, RNASeq, DifferentialExpression", "VignetteBuilder": "knitr", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:40:19 UTC", "RemoteUrl": "https://github.com/bioc/PROPER", "RemoteRef": "RELEASE_3_23", "RemoteSha": "1d8c9e7b6f826cfa268184667d97bfb9900d8620", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:26:16 UTC", "User": "root" }, "MD5sum": "da733092fa34e50c2a90f72c5a85061a", "_user": "bioc-release", "_type": "src", "_file": "PROPER_1.44.0.tar.gz", "_fileid": "12c5f5a798575a75b46400025ad4d194e07d93fd37c8102bcb6a69cbd9074adf", "_filesize": 2006321, "_sha256": "12c5f5a798575a75b46400025ad4d194e07d93fd37c8102bcb6a69cbd9074adf", "_created": "2026-05-29T07:26:16.000Z", "_published": "2026-05-29T08:31:51.719Z", "_jobs": [ { "job": 78456939024, "time": 160, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7285407409" }, { "job": 78456939013, "time": 186, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7285415104" }, { "job": 78456939020, "time": 217, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7285424275" }, { "job": 78456938997, "time": 124, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7286476535" }, { "job": 78456939019, "time": 88, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7286467002" }, { "job": 78456200013, "time": 324, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285357854" }, { "job": 78456939018, "time": 140, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285401266" }, { "job": 78456939030, "time": 172, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7285411395" }, { "job": 78456939025, "time": 115, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7285393907" }, { "job": 78456939040, "time": 112, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7285393231" } ], "_bioccheck": { "error": 2, "warning": 6, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623967683", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/PROPER", "_commit": { "id": "1d8c9e7b6f826cfa268184667d97bfb9900d8620", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380019 }, "_maintainer": { "name": "Hao Wu", "email": "hao.wu@emory.edu", "login": "haowulab", "description": "Distinguished Professor in Artificial Intelligence ", "uuid": 16678455 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3", "role": "Depends" }, { "package": "edgeR", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "DSS", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.0", "bioc": "3.24" }, { "branch": "release", "version": "1.44.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "sequencing", "rnaseq", "differentialexpression" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 451, "source": "https://www.bioconductor.org/packages/stats/bioc/PROPER" }, "_mentions": 25, "_searchresults": 25, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/PROPER.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "comparePower", "estParam", "plotAll", "plotFDcost", "plotFDR", "plotPower", "plotPowerAlpha", "plotPowerFD", "plotPowerHist", "plotPowerTD", "power.seqDepth", "RNAseq.SimOptions.2grp", "runSims", "simRNAseq", "summaryPower" ], "_datasets": [ { "name": "GE.human", "title": "Some existing RNA-seq and gene expression microarray data", "object": "GE.human", "file": "GE.human.RData", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "param", "title": "Some existing RNA-seq and gene expression microarray data", "object": "bottomly", "file": "bottomly.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "param", "title": "Some existing RNA-seq and gene expression microarray data", "object": "cheung", "file": "cheung.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "param", "title": "Some existing RNA-seq and gene expression microarray data", "object": "gilad", "file": "gilad.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "param", "title": "Some existing RNA-seq and gene expression microarray data", "object": "maqc", "file": "maqc.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "pbmc", "title": "Some existing RNA-seq and gene expression microarray data", "object": "pbmc", "file": "pbmc.RData", "class": [ "matrix", "array" ], "fields": [ "pbmc:pha-activated", "pbmc:normal" ], "rows": 22215, "table": true, "tojson": true } ], "_help": [ { "page": "comparePower", "title": "Compute the power-related quantities from simulation results", "topics": [ "comparePower" ] }, { "page": "estParam", "title": "estimate simulation parameters from a count table", "topics": [ "estParam" ] }, { "page": "historicalData", "title": "Some existing RNA-seq and gene expression microarray data", "topics": [ "bottomly", "cheung", "GE.human", "gilad", "maqc", "param", "pbmc" ] }, { "page": "plotPowerHist", "title": "Plot the histogram of power", "topics": [ "plotPowerHist" ] }, { "page": "plots", "title": "Plot the stratified curves for power-related quantities", "topics": [ "plotAll", "plotFDcost", "plotFDR", "plotPower", "plotPowerAlpha", "plotPowerFD", "plotPowerTD" ] }, { "page": "power.seqDepth", "title": "Estimate the marginal power under different sequencing depth", "topics": [ "power.seqDepth" ] }, { "page": "RNAseq.SimOptions.2grp", "title": "Set up options for simulating RNA-seq data in two-group comparison.", "topics": [ "RNAseq.SimOptions.2grp" ] }, { "page": "runSims", "title": "Run a number of RNA-seq simulations and DE detections", "topics": [ "runSims" ] }, { "page": "simRNAseq", "title": "Simulate RNA-seq count data", "topics": [ "simRNAseq" ] }, { "page": "summaryPower", "title": "Generate a summary table for power analysis result", "topics": [ "summaryPower" ] } ], "_rundeps": [ "edgeR", "lattice", "limma", "locfit", "statmod" ], "_vignettes": [ { "source": "PROPER.Rnw", "filename": "PROPER.pdf", "title": "Power and Sample size analysis for gene expression from RNA-seq", "engine": "knitr::knitr", "headings": [], "created": "2014-11-25 19:26:20", "modified": "2016-02-28 14:52:04", "commits": 2 } ], "_score": 5.176091259055681, "_indexed": false, "_nocasepkg": "proper", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/PROPER", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.44.0", "date": "2026-05-29T07:29:14.000Z", "distro": "noble", "commit": "1d8c9e7b6f826cfa268184667d97bfb9900d8620", "fileid": "cd81f7bff1f2853f8614d168dc2dc48973a37aae4ad5d1943d08be0dd987a26e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623967683" }, { "r": "4.6.0", "os": "linux", "version": "1.44.0", "date": "2026-05-29T07:29:48.000Z", "distro": "noble", "commit": "1d8c9e7b6f826cfa268184667d97bfb9900d8620", "fileid": "a691ec4f7453a659236fe0bf2fc3338bb4b6cb02bfc387abda29e49716739983", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623967683" }, { "r": "4.5.3", "os": "mac", "version": "1.44.0", "date": "2026-05-29T08:31:07.000Z", "commit": "1d8c9e7b6f826cfa268184667d97bfb9900d8620", "fileid": "747bcb06fb128f5d74d70a911df00fbb8a5a30bc1cd52ee13cf726ddeee7f2b3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623967683" }, { "r": "4.6.0", "os": "mac", "version": "1.44.0", "date": "2026-05-29T08:30:41.000Z", "commit": "1d8c9e7b6f826cfa268184667d97bfb9900d8620", "fileid": "49f20a5ee4a2ce03da5246e99dc05946b1e8fce50589ae2482619dc12783ee4c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623967683" }, { "r": "4.6.0", "os": "wasm", "version": "1.44.0", "date": "2026-05-29T07:28:55.000Z", "commit": "1d8c9e7b6f826cfa268184667d97bfb9900d8620", "fileid": "395b89d667c06692c8fdda76e5bb0075047f69400a74a7d8b29ff0a78b42a96a", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623967683" }, { "r": "4.7.0", "os": "win", "version": "1.44.0", "date": "2026-05-29T07:28:50.000Z", "commit": "1d8c9e7b6f826cfa268184667d97bfb9900d8620", "fileid": "4bf0a1c6ef960a4f5042d9918d45eebf76e5f23817e68cce4fa62189e77574d3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623967683" }, { "r": "4.5.3", "os": "win", "version": "1.44.0", "date": "2026-05-29T07:27:54.000Z", "commit": "1d8c9e7b6f826cfa268184667d97bfb9900d8620", "fileid": "39edf29e0aeb1c97385f8cd83220271054b49df5f5205587e4ecb3a1fa441b26", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623967683" }, { "r": "4.6.0", "os": "win", "version": "1.44.0", "date": "2026-05-29T07:27:49.000Z", "commit": "1d8c9e7b6f826cfa268184667d97bfb9900d8620", "fileid": "bd92d20e4626152f0cdeabd9422f8b97404dfd3c16c8766685ecdd1b77608cce", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623967683" } ] }