HTqPCR: Automated analysis of high-throughput qPCR data
Version 1.30.0

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
Bioconductor views DataImport DifferentialExpression GeneExpression MicrotitrePlateAssay MultipleComparison Preprocessing QualityControl Visualization qPCR
Date of publicationNone
MaintainerHeidi Dvinge <hdvinge@fredhutch.org>
LicenseArtistic-2.0
Version1.30.0
URL http://www.ebi.ac.uk/bertone/software
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("HTqPCR")

Getting started

Package overview

Popular man pages

filterCtData: Filter out features (genes) from qPCR data.
normalizeCtData: Normalization of Ct values from qPCR data.
plotCtHeatmap: Heatmap of qPCR Ct values.
plotCtPCA: PCA for qPCR Ct values.
plotCtScatter: Scatterplot of two sets of Ct values from qPCR data.
qPCRraw: Example raw qPCR data.
readCtData: Reading Ct values from qPCR experiments data into a qPCRset
See all...

All man pages Function index File listing

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

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

Files

DESCRIPTION
NAMESPACE
R
R/cbind.qPCRset.R
R/changeCtLayout.R
R/clusterCt.R
R/filterCategory.R
R/filterCtData.R
R/generics.R
R/heatmapSig.R
R/limmaCtData.R
R/mannwhitneyCtData.R
R/normalizeCtData.R
R/panel.Ct.cor.R
R/panel.Ct.scatter.R
R/plotCVBoxes.R
R/plotCtArray.R
R/plotCtBoxes.R
R/plotCtCard.R
R/plotCtCategory.R
R/plotCtCor.R
R/plotCtDensity.R
R/plotCtHeatmap.R
R/plotCtHistogram.R
R/plotCtLines.R
R/plotCtOverview.R
R/plotCtPCA.R
R/plotCtPairs.R
R/plotCtRQ.R
R/plotCtReps.R
R/plotCtScatter.R
R/plotCtSignificance.R
R/plotCtVariation.R
R/qPCRset.R
R/rbind.qPCRset.R
R/readCtData.R
R/setCategory.R
R/ttestCtData.R
build
build/vignette.rds
data
data/qPCRpros.RData
data/qPCRraw.RData
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/HTqPCR.R
inst/doc/HTqPCR.Rnw
inst/doc/HTqPCR.pdf
inst/exData
inst/exData/BioMark_sample.csv
inst/exData/CFX_sample.txt
inst/exData/LightCycler_sample.txt
inst/exData/OpenArray_sample.csv
inst/exData/SDS_sample.txt
inst/exData/files.txt
inst/exData/sample1.txt
inst/exData/sample2.txt
inst/exData/sample3.txt
inst/exData/sample4.txt
inst/exData/sample5.txt
inst/exData/sample6.txt
man
man/HTqPCR-package.Rd
man/cbind.Rd
man/changeCtLayout.Rd
man/clusterCt.Rd
man/filterCategory.Rd
man/filterCtData.Rd
man/heatmapSig.Rd
man/limmaCtData.Rd
man/mannwhitneyCtData.Rd
man/normalizeCtData.Rd
man/plotCVBoxes.Rd
man/plotCtArray.Rd
man/plotCtBoxes.Rd
man/plotCtCard.Rd
man/plotCtCategory.Rd
man/plotCtCor.Rd
man/plotCtDensity.Rd
man/plotCtHeatmap.Rd
man/plotCtHistogram.Rd
man/plotCtOverview.Rd
man/plotCtPCA.Rd
man/plotCtPairs.Rd
man/plotCtRQ.Rd
man/plotCtReps.Rd
man/plotCtScatter.Rd
man/plotCtSignificance.Rd
man/plotCtVariation.Rd
man/plotGenes.Rd
man/qPCRpros.Rd
man/qPCRraw.Rd
man/qPCRset-class.Rd
man/readCtData.Rd
man/setCategory.Rd
man/ttestCtData.Rd
vignettes
vignettes/HTqPCR-Bibliography.bib
vignettes/HTqPCR.Rnw
vignettes/objects.png
vignettes/workflow.png
HTqPCR documentation built on May 20, 2017, 10:28 p.m.

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