Package: ddCt 1.61.0
Jitao David Zhang
ddCt: The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.
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ddCt.pdf |ddCt.html✨
ddCt/json (API)
| # Install 'ddCt' in R: |
| install.packages('ddCt', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:ddCt-1.61.0(bioc 3.20)ddCt-1.60.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:1bfc606e94
Exports:assayDatabarchartbarploterrbarbrewer.palbrewer.pal.infoColMapcoreDatacoreData<-CtCt<-CtErrdCtdCtErrddCtddCtAbsoluteddCtErrddCtExpressionDEFAULT.CT.COLNAMEDEFAULT.FEATURE.COLNAMEDEFAULT.SAMPLE.COLNAMEdetectorNamesdetectorNames<-elistelistWriteerrBarchartexprsfDatafData<-featureDatafeatureData<-featureNamesfeatureNames<-fileNamesgetDirInputFramelevellevelErrnumberCtnumberNApanel.ablinepanel.barchartpanel.gridpanel.segmentspanel.textpDatapData<-phenoDataphenoData<-QuantStudioFramereadQuantStudioreadSDMremoveDetectorremoveNTCremoveSamplereplaceDetectorreplaceSamplereplaceVectorByEqualityrightCensoringsampleNamessampleNames<-SDMFrameTSVFrameuniqueDetectorNamesuniqueDetectorNames<-uniqueSampleNamesuniqueSampleNames<-varLabelsvarMetadatavarMetadata<-write.htmltablewriteSimpleTabCsvxtable
Dependencies:BiobaseBiocGenericslatticeRColorBrewerxtable
Analyse RT-PCR data with the end-to-end script in ddCt package
Rendered fromrtPCR-usage.Rnwusingutils::Sweaveon Jul 03 2024.Last update: 2013-11-01
Started: 2013-11-01
How to apply the ddCt method
Rendered fromRT-PCR-Script-ddCt.Rnwusingutils::Sweaveon Jul 03 2024.Last update: 2018-08-30
Started: 2013-11-01
Introduction to the ddCt method for qRT-PCR data analysis: background, algorithm and example
Rendered fromrtPCR.Rnwusingutils::Sweaveon Jul 03 2024.Last update: 2016-03-09
Started: 2013-11-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Barplot with error bars. | barploterrbar |
| absolute quantification for Taqman data | ddCtAbsolute |
| ddCt Expression | "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 |
| Apply the ddCt algorithm for a given data set | ddCtExpression ddCtExpression,InputFrame-method ddCtExpression,SDMFrame-method ddCtExpression-methods |
| Write ddCtExpression object into data frame or files | elist elistWrite summary |
| Draw barchart of relative expression level with error-bars | errBarchart errBarchart,ddCtExpression,character-method errBarchart,ddCtExpression,missing-method errBarchart-methods |
| Class "errBarchartParameter" | errBarchartParameter-class exprsUndeterminedLabel,errBarchartParameter-method show,errBarchartParameter-method |
| Auxillary functions for the executive scripts | getDir |
| Build an InputFrame from a ReaderClass or a data frame | InputFrame InputFrame,data.frame-method |
| Working with SDM files | $,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 |
| Class "InputReader" | ColMap InputReader-class QuantStudioReader-class SDMReader-class TSVFrame TSVReader-class |
| Read QuantStudio file(s) | QuantStudioFrame readQuantStudio |
| Remove NTC samples | removeNTC removeNTC,ddCtExpression-method removeNTC,InputFrame-method removeNTC-methods |
| REPLACE ITEMS OF VECTOR BY EQUALITY | replaceVectorByEquality |
| Read an SDM file | InputFrame,InputReader-method readSDM rightCensoring,InputFrame,numeric-method SDMFrame |
| Write a data frame into an html table within a html page | write.htmltable |
| Write a data frame into a tab delimited file | writeSimpleTabCsv |
