{ "_id": "6a103c23acfb0bcc41c9bd6f", "Package": "erccdashboard", "Type": "Package", "Title": "Assess Differential Gene Expression Experiments with ERCC\nControls", "Version": "1.47.0", "Author": "Sarah Munro, Steve Lund", "Maintainer": "Sarah Munro ", "Description": "Technical performance metrics for differential gene\nexpression experiments using External RNA Controls Consortium\n(ERCC) spike-in ratio mixtures.", "License": "GPL (>=2)", "Collate": "runDashboard.R initDat.R dashboardFile.R plotAdjust.R\nloadERCCInfo.R loadExpMeas.R getDesignMat.R normalizeDat.R\nprepERCCDat.R est_r_m.R dynRangePlot.R geneExprTest.R\ntestDECount.R testDEArray.R erccROC.R estLODR.R printLODRres.R\nsaveERCCPlots.R maSignal.R annotLODR.R", "biocViews": "ImmunoOncology, GeneExpression, Transcription,\nAlternativeSplicing, DifferentialExpression,\nDifferentialSplicing, Genetics, Microarray, mRNAMicroarray,\nRNASeq, BatchEffect, MultipleComparison, QualityControl", "LazyData": "yes", "VignetteBuilder": "knitr", "Packaged": { "Date": "2026-05-11 10:22:34 UTC", "User": "root" }, "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:39:36 UTC", "RemoteUrl": "https://github.com/bioc/erccdashboard", "RemoteRef": "HEAD", "RemoteSha": "c1b2812f6f9deddbb2de4adda69e19e09580b262", "NeedsCompilation": "no", "MD5sum": "62ee02f15ea1f645f4a218d09b826a7a", "_user": "bioc", "_type": "src", "_file": "erccdashboard_1.47.0.tar.gz", "_fileid": "01093f626f0793938aa79dc95ef83c612b29640a70b68ac7d1d440794b9d7f01", "_filesize": 1940098, "_sha256": "01093f626f0793938aa79dc95ef83c612b29640a70b68ac7d1d440794b9d7f01", "_created": "2026-05-11T10:22:34.000Z", "_published": "2026-05-22T11:21:07.474Z", "_jobs": [ { "job": 77369358618, "time": 157, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "6916021828" }, { "job": 77369358584, "time": 227, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6916044546" }, { "job": 77369359158, "time": 179, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6916030843" }, { "job": 77369358969, "time": 124, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6916039439" }, { "job": 77369359047, "time": 134, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6916044601" }, { "job": 77369358432, "time": 208, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6915969263" }, { "job": 77369358362, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159268815" }, { "job": 77369359133, "time": 106, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "6916004654" }, { "job": 77369359250, "time": 109, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "6916006005" }, { "job": 77369358879, "time": 127, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6916011915" } ], "_bioccheck": { "error": 1, "warning": 3, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25664247202", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/erccdashboard", "_commit": { "id": "c1b2812f6f9deddbb2de4adda69e19e09580b262", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379976 }, "_maintainer": { "name": "Sarah Munro", "email": "sarah.munro@gmail.com", "login": "munrosa", "uuid": 4389536 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "ggplot2", "version": ">= 2.1.0", "role": "Depends" }, { "package": "gridExtra", "version": ">= 2.0.0", "role": "Depends" }, { "package": "edgeR", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "gtools", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "locfit", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "qvalue", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "ROCR", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.47.0", "bioc": "3.24" }, { "branch": "release", "version": "1.46.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "geneexpression", "transcription", "alternativesplicing", "differentialexpression", "differentialsplicing", "genetics", "microarray", "mrnamicroarray", "rnaseq", "batcheffect", "multiplecomparison", "qualitycontrol" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 420, "source": "https://www.bioconductor.org/packages/stats/bioc/erccdashboard" }, "_mentions": 3, "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/erccdashboard.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_homeurl": "https://github.com/munrosa/erccdashboard", "_realowner": "bioc", "_cranurl": false, "_exports": [ "annotLODR", "dynRangePlot", "erccROC", "est_r_m", "estLODR", "geneExprTest", "initDat", "maSignal", "runDashboard", "saveERCCPlots" ], "_datasets": [ { "name": "ERCCDef", "title": "ERCCDef dataframe", "object": "ERCC", "class": [ "data.frame" ], "fields": [ "Feature", "Length", "GC" ], "rows": 96, "table": true, "tojson": true }, { "name": "ERCCMix1and2", "title": "ERCCMix1and2 dataframe", "object": "ERCC", "class": [ "data.frame" ], "fields": [ "ERCC.AMB.Expected", "Subpool", "Mix1Conc.Attomoles_ul", "Mix2Conc.Attomoles_ul" ], "rows": 96, "table": true, "tojson": true }, { "name": "MET.CTL.countDat", "title": "Rat toxicogenomics count data", "object": "SEQC.Example", "class": [ "data.frame" ], "fields": [ "Feature", "MET_1", "MET_2", "MET_3", "CTL_1", "CTL_2", "CTL_3" ], "rows": 16590, "table": true, "tojson": true }, { "name": "MET.CTL.totalReads", "title": "Rat toxicogenomics total read data", "object": "SEQC.Example", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "UHRR.HBRR.arrayDat", "title": "UHRR and HBRR Illumina BeadArray data", "object": "SEQC.Example", "class": [ "data.frame" ], "fields": [ "Feature", "UHRR_3", "UHRR_2", "UHRR_1", "HBRR_3", "HBRR_2", "HBRR_1" ], "rows": 17627, "table": true, "tojson": true }, { "name": "UHRR.HBRR.countDat", "title": "UHRR and HBRR RNA-Seq Illumina count data", "object": "SEQC.Example", "class": [ "data.frame" ], "fields": [ "Feature", "UHRR_1", "UHRR_2", "UHRR_3", "UHRR_4", "HBRR_1", "HBRR_2", "HBRR_3", "HBRR_4" ], "rows": 43919, "table": true, "tojson": true }, { "name": "UHRR.HBRR.totalReads", "title": "UHRR and HBRR sample total read data", "object": "SEQC.Example", "class": [ "integer" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "annotLODR", "title": "Annotate signal-abundance and ratio-abundance plots with LODR", "topics": [ "annotLODR" ] }, { "page": "dynRangePlot", "title": "Produce signal-abundance plot to evaluate dynamic range", "topics": [ "dynRangePlot" ] }, { "page": "ERCC", "title": "ERCC data", "topics": [ "ERCC" ] }, { "page": "ERCCDef", "title": "ERCCDef dataframe", "topics": [ "ERCCDef" ] }, { "page": "ERCCMix1and2", "title": "ERCCMix1and2 dataframe", "topics": [ "ERCCMix1and2" ] }, { "page": "erccROC", "title": "Produce Receiver Operator Characteristic (ROC) Curves and AUC statistics", "topics": [ "erccROC" ] }, { "page": "est_r_m", "title": "Estimate the mRNA fraction differences for the pair of samples using replicate data", "topics": [ "est_r_m" ] }, { "page": "estLODR", "title": "Estimate Limit of Detection of Ratios (LODR)", "topics": [ "estLODR" ] }, { "page": "geneExprTest", "title": "Prepare differential expression testing results for spike-in analysis", "topics": [ "geneExprTest" ] }, { "page": "initDat", "title": "Initialize the exDat list", "topics": [ "initDat" ] }, { "page": "maSignal", "title": "Generate MA plots with or without annotation using LODR estimates", "topics": [ "maSignal" ] }, { "page": "MET.CTL.countDat", "title": "Rat toxicogenomics count data", "topics": [ "MET.CTL.countDat" ] }, { "page": "MET.CTL.totalReads", "title": "Rat toxicogenomics total read data", "topics": [ "MET.CTL.totalReads" ] }, { "page": "runDashboard", "title": "Run default erccdashboard analysis of ERCC control ratio mixtures", "topics": [ "runDashboard" ] }, { "page": "saveERCCPlots", "title": "Save erccdashboard plots to a pdf file", "topics": [ "saveERCCPlots" ] }, { "page": "SEQC.Example", "title": "Example data from SEQC project for erccdashboard analysis", "topics": [ "SEQC.Example" ] }, { "page": "UHRR.HBRR.arrayDat", "title": "UHRR and HBRR Illumina BeadArray data", "topics": [ "UHRR.HBRR.arrayDat" ] }, { "page": "UHRR.HBRR.countDat", "title": "UHRR and HBRR RNA-Seq Illumina count data", "topics": [ "UHRR.HBRR.countDat" ] }, { "page": "UHRR.HBRR.totalReads", "title": "UHRR and HBRR sample total read data", "topics": [ "UHRR.HBRR.totalReads" ] } ], "_rundeps": [ "bitops", "caTools", "cli", "cpp11", "edgeR", "evaluate", "farver", "ggplot2", "glue", "gplots", "gridExtra", "gtable", "gtools", "highr", "isoband", "KernSmooth", "knitr", "labeling", "lattice", "lifecycle", "limma", "locfit", "magrittr", "MASS", "plyr", "qvalue", "R6", "RColorBrewer", "Rcpp", "reshape2", "rlang", "ROCR", "S7", "scales", "statmod", "stringi", "stringr", "vctrs", "viridisLite", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "erccdashboard.Rmd", "filename": "erccdashboard.html", "title": "Assessing Differential Gene Expression Experiments with the erccdashboard", "author": "Sarah Munro, Steve Lund", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Example: Rat Toxicogenomics", "Load Example Data", "Define Input Parameters", "Run Example and View Output", "Comparison of Performance Between Experiments", "UHRR vs. HBRR Microarray Experiment", "UHRR vs. HBRR RNA-Seq Experiment", "Analysis Details and Options", "Flexibility in Differential Expression Testing", "LODR Estimation Options", "Printing Plots to File", "Analysis of Alternative Spike-in Designs", "R version and sessionInfo() output" ], "created": "2024-10-26 01:09:25", "modified": "2024-10-26 01:09:25", "commits": 1 } ], "_score": 3.778151250383644, "_indexed": true, "_nocasepkg": "erccdashboard", "_universes": [ "bioc", "munrosa" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-05-11T10:25:54.000Z", "distro": "noble", "commit": "c1b2812f6f9deddbb2de4adda69e19e09580b262", "fileid": "646ca897bda656c2f99ad4559d117f3ebf112ea31003af2fe811fd52e2800371", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25664247202" }, { "r": "4.6.0", "os": "linux", "version": "1.47.0", "date": "2026-05-11T10:25:15.000Z", "distro": "noble", "commit": "c1b2812f6f9deddbb2de4adda69e19e09580b262", "fileid": "dfaf707fbbe10444de566fad48040203664d7d79a688f6738b74ac635c1a1054", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25664247202" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-05-11T10:25:54.000Z", "commit": "c1b2812f6f9deddbb2de4adda69e19e09580b262", "fileid": "a4ff4918263b737e1692cd785b5a1934736e339010ac9c3d866af93e38e9a99b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25664247202" }, { "r": "4.6.0", "os": "mac", "version": "1.47.0", "date": "2026-05-11T10:25:58.000Z", "commit": "c1b2812f6f9deddbb2de4adda69e19e09580b262", "fileid": "d11a2c644ba6495b8cd5b48f875af5610ebe37dc42d28715b239ddf498614dab", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25664247202" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-05-11T10:23:50.000Z", "commit": "c1b2812f6f9deddbb2de4adda69e19e09580b262", "fileid": "c2f387920fcf79bb5fd96637b719a5432398ab2641eb85bc308e81f86a5d7569", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25664247202" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-05-11T10:23:49.000Z", "commit": "c1b2812f6f9deddbb2de4adda69e19e09580b262", "fileid": "b1e05c1d013d775f2bd4237ce40f16b22a3275ca6b5c5a9003a19a3692d7b7ae", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25664247202" }, { "r": "4.6.0", "os": "win", "version": "1.47.0", "date": "2026-05-11T10:24:10.000Z", "commit": "c1b2812f6f9deddbb2de4adda69e19e09580b262", "fileid": "3a23b0f2da5aac7c1b310ba23c78f135602f1e905128c5a0bdd58dedb895ab0e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25664247202" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-05-22T11:20:47.000Z", "commit": "c1b2812f6f9deddbb2de4adda69e19e09580b262", "fileid": "775914d711c68d2138e6abd2de0787e937468f575b01e0bbe270371af92a16e1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25664247202" } ] }