HTqPCR: Automated analysis of high-throughput qPCR data

Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).

AuthorHeidi Dvinge, Paul Bertone
Date of publicationNone
MaintainerHeidi Dvinge <hdvinge@fredhutch.org>
LicenseArtistic-2.0
Version1.28.0
http://www.ebi.ac.uk/bertone/software

View on Bioconductor

Man pages

cbind: Combine qPCRset objects

changeCtLayout: Changing the dimensions (rows x columns) of qPCRset objects

clusterCt: Clustering of qPCR Ct values

filterCategory: Filter Ct values based on their feature categories.

filterCtData: Filter out features (genes) from qPCR data.

heatmapSig: Heatmap of deltadeltaCt values from qPCR data.

HTqPCR-package: Analysis of High-Throughput qPCR data (HTqPCR)

limmaCtData: Differentially expressed features with qPCR: limma

mannwhitneyCtData: Differentially expressed features with qPCR: Mann-Whitney

normalizeCtData: Normalization of Ct values from qPCR data.

plotCtArray: Image plot of qPCR Ct values from an array format

plotCtBoxes: Boxplots for qPCR Ct values.

plotCtCard: Image plot of qPCR Ct values from a card format

plotCtCategory: Summarising the feature categories for Ct values.

plotCtCor: Correlation between Ct values from qPCR data

plotCtDensity: Distribution plot for qPCR Ct values.

plotCtHeatmap: Heatmap of qPCR Ct values.

plotCtHistogram: Histrogram of Ct values from qPCR experiments.

plotCtOverview: Overview plot of qPCR Ct values across multiple conditions.

plotCtPairs: Pairwise scatterplot of multiple sets of Ct values from qPCR...

plotCtPCA: PCA for qPCR Ct values.

plotCtReps: Scatter plot of features analysed twice during each qPCR...

plotCtRQ: Plot the relative quantification of Ct values from qPCR...

plotCtScatter: Scatterplot of two sets of Ct values from qPCR data.

plotCtSignificance: Barplot with Ct values between genes from qPCR.

plotCtVariation: Plot variation in Ct values across replicates

plotCVBoxes: Boxplots of CV for qPCR Ct values.

plotGenes: Plotting Ct values from qPCR across multiple samples.

qPCRpros: Example processed qPCR data

qPCRraw: Example raw qPCR data.

qPCRset-class: Class "qPCRset"

readCtData: Reading Ct values from qPCR experiments data into a qPCRset

setCategory: Assign categories to Ct values from qPCR data.

ttestCtData: Differentially expressed features with qPCR: t-test

Functions

cbind Man page
cbind.qPCRset Man page
changeCtLayout Man page
clusterCt Man page
exprs<-,qPCRset,ANY-method Man page
exprs,qPCRset-method Man page
featureCategory Man page
featureCategory<- Man page
featureCategory<-,qPCRset-method Man page
featureCategory,qPCRset-method Man page
featureClass Man page
featureClass<- Man page
featureClass<-,qPCRset-method Man page
featureClass,qPCRset-method Man page
featureNames<-,qPCRset,character-method Man page
featureNames,qPCRset-method Man page
featurePos Man page
featurePos<- Man page
featurePos<-,qPCRset-method Man page
featurePos,qPCRset-method Man page
featureType Man page
featureType<- Man page
featureType<-,qPCRset-method Man page
featureType,qPCRset-method Man page
filterCategory Man page
filterCtData Man page
flag Man page
flag<- Man page
flag<-,qPCRset-method Man page
flag,qPCRset-method Man page
getCt Man page
getCtHistory Man page
heatmapSig Man page
HTqPCR Man page
HTqPCR-package Man page
limmaCtData Man page
mannwhitneyCtData Man page
normalizeCtData Man page
n.samples Man page
n.wells Man page
plotCtArray Man page
plotCtBoxes Man page
plotCtCard Man page
plotCtCategory Man page
plotCtCor Man page
plotCtDensity Man page
plotCtHeatmap Man page
plotCtHistogram Man page
plotCtLines Man page
plotCtOverview Man page
plotCtPairs Man page
plotCtPCA Man page
plotCtReps Man page
plotCtRQ Man page
plotCtScatter Man page
plotCtSignificance Man page
plotCtVariation Man page
plotCVBoxes Man page
qPCRpros Man page
qPCRraw Man page
qPCRset-class Man page
[,qPCRset-method Man page
rbind Man page
rbind.qPCRset Man page
.readCtBioMark Man page
.readCtCFX Man page
readCtData Man page
.readCtLightCycler Man page
.readCtOpenArray Man page
.readCtPlain Man page
.readCtSDS Man page
sampleNames<-,qPCRset,character-method Man page
sampleNames,qPCRset-method Man page
setCategory Man page
setCt<- Man page
setCtHistory<- Man page
show,qPCRset-method Man page
summary,qPCRset-method Man page
ttestCtData Man page

Files

HTqPCR/DESCRIPTION
HTqPCR/NAMESPACE
HTqPCR/R
HTqPCR/R/cbind.qPCRset.R HTqPCR/R/changeCtLayout.R HTqPCR/R/clusterCt.R HTqPCR/R/filterCategory.R HTqPCR/R/filterCtData.R HTqPCR/R/generics.R HTqPCR/R/heatmapSig.R HTqPCR/R/limmaCtData.R HTqPCR/R/mannwhitneyCtData.R HTqPCR/R/normalizeCtData.R HTqPCR/R/panel.Ct.cor.R HTqPCR/R/panel.Ct.scatter.R HTqPCR/R/plotCVBoxes.R HTqPCR/R/plotCtArray.R HTqPCR/R/plotCtBoxes.R HTqPCR/R/plotCtCard.R HTqPCR/R/plotCtCategory.R HTqPCR/R/plotCtCor.R HTqPCR/R/plotCtDensity.R HTqPCR/R/plotCtHeatmap.R HTqPCR/R/plotCtHistogram.R HTqPCR/R/plotCtLines.R HTqPCR/R/plotCtOverview.R HTqPCR/R/plotCtPCA.R HTqPCR/R/plotCtPairs.R HTqPCR/R/plotCtRQ.R HTqPCR/R/plotCtReps.R HTqPCR/R/plotCtScatter.R HTqPCR/R/plotCtSignificance.R HTqPCR/R/plotCtVariation.R HTqPCR/R/qPCRset.R HTqPCR/R/rbind.qPCRset.R HTqPCR/R/readCtData.R HTqPCR/R/setCategory.R HTqPCR/R/ttestCtData.R
HTqPCR/build
HTqPCR/build/vignette.rds
HTqPCR/data
HTqPCR/data/qPCRpros.RData
HTqPCR/data/qPCRraw.RData
HTqPCR/inst
HTqPCR/inst/CITATION
HTqPCR/inst/NEWS
HTqPCR/inst/doc
HTqPCR/inst/doc/HTqPCR.R
HTqPCR/inst/doc/HTqPCR.Rnw
HTqPCR/inst/doc/HTqPCR.pdf
HTqPCR/inst/exData
HTqPCR/inst/exData/BioMark_sample.csv
HTqPCR/inst/exData/CFX_sample.txt
HTqPCR/inst/exData/LightCycler_sample.txt
HTqPCR/inst/exData/OpenArray_sample.csv
HTqPCR/inst/exData/SDS_sample.txt
HTqPCR/inst/exData/files.txt
HTqPCR/inst/exData/sample1.txt
HTqPCR/inst/exData/sample2.txt
HTqPCR/inst/exData/sample3.txt
HTqPCR/inst/exData/sample4.txt
HTqPCR/inst/exData/sample5.txt
HTqPCR/inst/exData/sample6.txt
HTqPCR/man
HTqPCR/man/HTqPCR-package.Rd HTqPCR/man/cbind.Rd HTqPCR/man/changeCtLayout.Rd HTqPCR/man/clusterCt.Rd HTqPCR/man/filterCategory.Rd HTqPCR/man/filterCtData.Rd HTqPCR/man/heatmapSig.Rd HTqPCR/man/limmaCtData.Rd HTqPCR/man/mannwhitneyCtData.Rd HTqPCR/man/normalizeCtData.Rd HTqPCR/man/plotCVBoxes.Rd HTqPCR/man/plotCtArray.Rd HTqPCR/man/plotCtBoxes.Rd HTqPCR/man/plotCtCard.Rd HTqPCR/man/plotCtCategory.Rd HTqPCR/man/plotCtCor.Rd HTqPCR/man/plotCtDensity.Rd HTqPCR/man/plotCtHeatmap.Rd HTqPCR/man/plotCtHistogram.Rd HTqPCR/man/plotCtOverview.Rd HTqPCR/man/plotCtPCA.Rd HTqPCR/man/plotCtPairs.Rd HTqPCR/man/plotCtRQ.Rd HTqPCR/man/plotCtReps.Rd HTqPCR/man/plotCtScatter.Rd HTqPCR/man/plotCtSignificance.Rd HTqPCR/man/plotCtVariation.Rd HTqPCR/man/plotGenes.Rd HTqPCR/man/qPCRpros.Rd HTqPCR/man/qPCRraw.Rd HTqPCR/man/qPCRset-class.Rd HTqPCR/man/readCtData.Rd HTqPCR/man/setCategory.Rd HTqPCR/man/ttestCtData.Rd
HTqPCR/vignettes
HTqPCR/vignettes/HTqPCR-Bibliography.bib
HTqPCR/vignettes/HTqPCR.Rnw
HTqPCR/vignettes/objects.png
HTqPCR/vignettes/workflow.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.