Package: ddCt 1.63.0

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.

Authors:Jitao David Zhang, Rudolf Biczok, and Markus Ruschhaupt

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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'))

Peer review:

On BioConductor:ddCt-1.63.0(bioc 3.21)ddCt-1.62.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpressiondifferentialexpressionmicrotitreplateassayqpcr

4.38 score 8 scripts 296 downloads 4 mentions 72 exports 6 dependencies

Last updated 2 months agofrom:3e97954ec1. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winWARNINGNov 29 2024
R-4.5-linuxWARNINGNov 29 2024
R-4.4-winWARNINGNov 29 2024
R-4.4-macWARNINGNov 29 2024
R-4.3-winWARNINGNov 29 2024
R-4.3-macWARNINGNov 29 2024

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:BiobaseBiocGenericsgenericslatticeRColorBrewerxtable

Analyse RT-PCR data with the end-to-end script in ddCt package

Rendered fromrtPCR-usage.Rnwusingutils::Sweaveon Nov 29 2024.

Last update: 2013-11-01
Started: 2013-11-01

How to apply the ddCt method

Rendered fromRT-PCR-Script-ddCt.Rnwusingutils::Sweaveon Nov 29 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 Nov 29 2024.

Last update: 2016-03-09
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Barplot with error bars.barploterrbar
absolute quantification for Taqman dataddCtAbsolute
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 setddCtExpression ddCtExpression,InputFrame-method ddCtExpression,SDMFrame-method ddCtExpression-methods
Write ddCtExpression object into data frame or fileselist elistWrite summary
Draw barchart of relative expression level with error-barserrBarchart 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 scriptsgetDir
Build an InputFrame from a ReaderClass or a data frameInputFrame 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 samplesremoveNTC removeNTC,ddCtExpression-method removeNTC,InputFrame-method removeNTC-methods
REPLACE ITEMS OF VECTOR BY EQUALITYreplaceVectorByEquality
Read an SDM fileInputFrame,InputReader-method readSDM rightCensoring,InputFrame,numeric-method SDMFrame
Write a data frame into an html table within a html pagewrite.htmltable
Write a data frame into a tab delimited filewriteSimpleTabCsv