# Automated analysis of high-throughput qPCR data

## Documentation for package ‘HTqPCR’ version 1.41.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

HTqPCR-package | Analysis of High-Throughput qPCR data (HTqPCR)
.readCtBioMark | Reading Ct values from qPCR experiments data into a qPCRset
.readCtCFX | Reading Ct values from qPCR experiments data into a qPCRset
.readCtLightCycler | Reading Ct values from qPCR experiments data into a qPCRset
.readCtOpenArray | Reading Ct values from qPCR experiments data into a qPCRset
.readCtPlain | Reading Ct values from qPCR experiments data into a qPCRset
.readCtSDS | Reading Ct values from qPCR experiments data into a qPCRset
cbind | Combine qPCRset objects
cbind.qPCRset | Combine qPCRset objects
changeCtLayout | Changing the dimensions (rows x columns) of qPCRset objects
clusterCt | Clustering of qPCR Ct values
exprs-method | Class "qPCRset"
exprs<--method | Class "qPCRset"
featureCategory | Class "qPCRset"
featureCategory-method | Class "qPCRset"
featureCategory<- | Class "qPCRset"
featureCategory<--method | Class "qPCRset"
featureClass | Class "qPCRset"
featureClass-method | Class "qPCRset"
featureClass<- | Class "qPCRset"
featureClass<--method | Class "qPCRset"
featureNames-method | Class "qPCRset"
featureNames<--method | Class "qPCRset"
featurePos | Class "qPCRset"
featurePos-method | Class "qPCRset"
featurePos<- | Class "qPCRset"
featurePos<--method | Class "qPCRset"
featureType | Class "qPCRset"
featureType-method | Class "qPCRset"
featureType<- | Class "qPCRset"
featureType<--method | Class "qPCRset"
filterCategory | Filter Ct values based on their feature categories.
filterCtData | Filter out features (genes) from qPCR data.
flag | Class "qPCRset"
flag-method | Class "qPCRset"
flag<- | Class "qPCRset"
flag<--method | Class "qPCRset"
getCt | Class "qPCRset"
getCtHistory | Class "qPCRset"
heatmapSig | Heatmap of deltadeltaCt values from qPCR data.
HTqPCR | Analysis of High-Throughput qPCR data (HTqPCR)
limmaCtData | Differentially expressed features with qPCR: limma
mannwhitneyCtData | Differentially expressed features with qPCR: Mann-Whitney
n.samples | Class "qPCRset"
n.wells | Class "qPCRset"
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.
plotCtLines | Plotting Ct values from qPCR across multiple samples.
plotCtOverview | Overview plot of qPCR Ct values across multiple conditions.
plotCtPairs | Pairwise scatterplot of multiple sets of Ct values from qPCR data.
plotCtPCA | PCA for qPCR Ct values.
plotCtReps | Scatter plot of features analysed twice during each qPCR experiment.
plotCtRQ | Plot the relative quantification of Ct values from qPCR experiments.
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.
qPCRpros | Example processed qPCR data
qPCRraw | Example raw qPCR data.
qPCRset-class | Class "qPCRset"
rbind | Combine qPCRset objects
rbind.qPCRset | Combine qPCRset objects
readCtData | Reading Ct values from qPCR experiments data into a qPCRset
sampleNames-method | Class "qPCRset"
sampleNames<--method | Class "qPCRset"
setCategory | Assign categories to Ct values from qPCR data.
setCt<- | Class "qPCRset"
setCtHistory<- | Class "qPCRset"
show-method | Class "qPCRset"
summary-method | Class "qPCRset"
ttestCtData | Differentially expressed features with qPCR: t-test
[-method | Class "qPCRset"