{ "_id": "6a19459eacfb0bcc41dd8cda", "Package": "ddCt", "Title": "The ddCt Algorithm for the Analysis of Quantitative Real-Time\nPCR (qRT-PCR)", "Version": "1.68.0", "Date": "2021-07-30", "Author": "Jitao David Zhang, Rudolf Biczok, and Markus Ruschhaupt", "Description": "The Delta-Delta-Ct (ddCt) Algorithm is an approximation\nmethod to determine relative gene expression with quantitative\nreal-time PCR (qRT-PCR) experiments. Compared to other\napproaches, it requires no standard curve for each\nprimer-target pair, therefore reducing the working load and yet\nreturning accurate enough results as long as the assumptions of\nthe amplification efficiency hold. The ddCt package implements\na pipeline to collect, analyse and visualize qRT-PCR results,\nfor example those from TaqMan SDM software, mainly using the\nddCt method. The pipeline can be either invoked by a script in\ncommand-line or through the API consisting of S4-Classes,\nmethods and functions.", "Maintainer": "Jitao David Zhang ", "biocViews": "GeneExpression, DifferentialExpression,\nMicrotitrePlateAssay, qPCR", "License": "LGPL-3", "Collate": "AllGlobals.R AllClasses.R AllGenerics.R AllFunctions.R\nAllMethods.R absoluteQ.R ddCtSplit.R output.R visualization.R", "Config/testthat/edition": "3", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:34:05 UTC", "RemoteUrl": "https://github.com/bioc/ddCt", "RemoteRef": "RELEASE_3_23", "RemoteSha": "e384cc4a22aa6088a19b84f7878d9abc43cae077", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 06:51:21 UTC", "User": "root" }, "MD5sum": "dce4b5b78364ef6887e7ac0983cc62fc", "_user": "bioc-release", "_type": "src", "_file": "ddCt_1.68.0.tar.gz", "_fileid": "2bd2f2fe17e9f66a5aa3be614ef7c508f28afdaf986cb2f9e82fb89d48e40c2b", "_filesize": 946124, "_sha256": 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Biologist in Drug Discovery", "uuid": 1397024 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.3.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "Biobase", "version": ">= 1.10.0", "role": "Imports" }, { "package": "RColorBrewer", "version": ">= 0.1-3", "role": "Imports" }, { "package": "xtable", "role": "Imports" }, { "package": "lattice", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.69.0", "bioc": "3.24" }, { "branch": "release", "version": "1.68.0", "bioc": "3.23" } ], "_topics": [ "geneexpression", "differentialexpression", "microtitreplateassay", "qpcr" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 504, "source": "https://www.bioconductor.org/packages/stats/bioc/ddCt" }, "_mentions": 4, "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ddCt.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "assayData", "barchart", "barploterrbar", "brewer.pal", "brewer.pal.info", "ColMap", "coreData", "coreData<-", "Ct", "Ct<-", "CtErr", "dCt", "dCtErr", "ddCt", "ddCtAbsolute", "ddCtErr", "ddCtExpression", "DEFAULT.CT.COLNAME", "DEFAULT.FEATURE.COLNAME", "DEFAULT.SAMPLE.COLNAME", "detectorNames", "detectorNames<-", "elist", "elistWrite", "errBarchart", "exprs", "fData", "fData<-", "featureData", "featureData<-", "featureNames", "featureNames<-", "fileNames", "getDir", "InputFrame", "level", "levelErr", "numberCt", "numberNA", "panel.abline", "panel.barchart", "panel.grid", "panel.segments", "panel.text", "pData", "pData<-", "phenoData", "phenoData<-", "QuantStudioFrame", "readQuantStudio", "readSDM", "removeDetector", "removeNTC", "removeSample", "replaceDetector", "replaceSample", "replaceVectorByEquality", "rightCensoring", "sampleNames", "sampleNames<-", "SDMFrame", "TSVFrame", "uniqueDetectorNames", "uniqueDetectorNames<-", "uniqueSampleNames", "uniqueSampleNames<-", "varLabels", "varMetadata", "varMetadata<-", "write.htmltable", "writeSimpleTabCsv", "xtable" ], "_help": [ { "page": "barploterrbar", "title": "Barplot with error bars.", "topics": [ "barploterrbar" ] }, { "page": "ddCtAbsolute", "title": "absolute quantification for Taqman data", "topics": [ "ddCtAbsolute" ] }, { "page": "ddCtExpression-class", "title": "ddCt Expression", "topics": [ "\"fData<-\"", "\"featureData<-\"", "\"featureNames<-\"", "\"pData<-\"", "\"phenoData<-\"", "\"varMetadata<-\"", "assayData", "barchart", "brewer.pal", "brewer.pal.info", "Ct", "Ct,ddCtExpression-method", "CtErr", "CtErr,ddCtExpression-method", "dCt", "dCt,ddCtExpression-method", "dCtErr", "dCtErr,ddCtExpression-method", "ddCt", "ddCt,ddCtExpression-method", "ddCtErr", "ddCtErr,ddCtExpression-method", "ddCtExpression-class", "elist,ddCtExpression-method", "elistWrite,ddCtExpression,character-method", "exprs", "fData", "featureData", "featureNames", "level", "level,ddCtExpression-method", "levelErr", "levelErr,ddCtExpression-method", "numberCt", "numberCt,ddCtExpression-method", "numberNA", "numberNA,ddCtExpression-method", "panel.abline", "panel.barchart", "panel.grid", "panel.segments", "panel.text", "pData", "phenoData", "varLabels", "varMetadata", "xtable" ] }, { "page": "ddCtExpression-methods", "title": "Apply the ddCt algorithm for a given data set", "topics": [ "ddCtExpression", "ddCtExpression,InputFrame-method", "ddCtExpression,SDMFrame-method", "ddCtExpression-methods" ] }, { "page": "elistWrite-methods", "title": "Write ddCtExpression object into data frame or files", "topics": [ "elist", "elistWrite", "summary" ] }, { "page": "errBarchart-methods", "title": "Draw barchart of relative expression level with error-bars", "topics": [ "errBarchart", "errBarchart,ddCtExpression,character-method", "errBarchart,ddCtExpression,missing-method", "errBarchart-methods" ] }, { "page": "errBarchartParameter-class", "title": "Class \"errBarchartParameter\"", "topics": [ "errBarchartParameter-class", "exprsUndeterminedLabel,errBarchartParameter-method", "show,errBarchartParameter-method" ] }, { "page": "getDir", "title": "Auxillary functions for the executive scripts", "topics": [ "getDir" ] }, { "page": "InputFrame", "title": "Build an InputFrame from a ReaderClass or a data frame", "topics": [ "InputFrame", "InputFrame,data.frame-method" ] }, { "page": "SDMFrame-class", "title": "Working with SDM files", "topics": [ "$,InputFrame-method", "ColMap-class", "coreData", "coreData,InputFrame-method", "coreData<-", "coreData<-,InputFrame,data.frame-method", "Ct,InputFrame-method", "Ct<-", "Ct<-,InputFrame,numeric-method", "DEFAULT.CT.COLNAME", "DEFAULT.FEATURE.COLNAME", "DEFAULT.SAMPLE.COLNAME", "detectorNames", "detectorNames,InputFrame-method", "detectorNames<-", "detectorNames<-,InputFrame,character-method", "fileNames", "fileNames,InputFrame-method", "InputFrame-class", "names,InputFrame-method", "removeDetector", "removeDetector,InputFrame,character-method", "removeDetector-methods", "removeSample", "removeSample,InputFrame,character-method", "removeSample-methods", "replaceDetector", "replaceDetector,InputFrame,character,character-method", "replaceDetector-methods", "replaceSample", "replaceSample,InputFrame,character,character-method", "replaceSample-methods", "rightCensoring", "rightCensoring,SDMFrame,numeric-method", "sampleNames", "sampleNames,InputFrame-method", "sampleNames<-", "sampleNames<-,InputFrame,character-method", "SDMFrame-class", "show,InputFrame-method", "uniqueDetectorNames", "uniqueDetectorNames,InputFrame-method", "uniqueDetectorNames<-", "uniqueDetectorNames<-,InputFrame,character,character-method", "uniqueDetectorNames<-,InputFrame,missing,character-method", "uniqueSampleNames", "uniqueSampleNames,InputFrame-method", "uniqueSampleNames<-", "uniqueSampleNames<-,InputFrame,character,character-method", "uniqueSampleNames<-,InputFrame,missing,character-method", "[,InputFrame-method", "[[,InputFrame-method" ] }, { "page": "InputReader-class", "title": "Class \"InputReader\"", "topics": [ "ColMap", "InputReader-class", "QuantStudioReader-class", "SDMReader-class", "TSVFrame", "TSVReader-class" ] }, { "page": "QuantStudioFrame", "title": "Read QuantStudio file(s)", "topics": [ "QuantStudioFrame", "readQuantStudio" ] }, { "page": "removeNTC-methods", "title": "Remove NTC samples", "topics": [ "removeNTC", "removeNTC,ddCtExpression-method", "removeNTC,InputFrame-method", "removeNTC-methods" ] }, { "page": "replaceVectorByEquality", "title": "REPLACE ITEMS OF VECTOR BY EQUALITY", "topics": [ "replaceVectorByEquality" ] }, { "page": "SDMFrame", "title": "Read an SDM file", "topics": [ "InputFrame,InputReader-method", "readSDM", "rightCensoring,InputFrame,numeric-method", "SDMFrame" ] }, { "page": "write.htmltable", "title": "Write a data frame into an html table within a html page", "topics": [ "write.htmltable" ] }, { "page": "writeSimpleTabCsv", "title": "Write a data frame into a tab delimited file", "topics": [ "writeSimpleTabCsv" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "generics", "lattice", "RColorBrewer", "xtable" ], "_vignettes": [ { "source": "rtPCR-usage.Rnw", "filename": "rtPCR-usage.pdf", "title": "Analyse RT-PCR data with the end-to-end script in ddCt package", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:09:24", "modified": "2013-11-01 20:09:24", "commits": 1 }, { "source": 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