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HTqPCR (version 1.26.0)

Automated analysis of high-throughput qPCR data

Description

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).

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Version

Version

1.26.0

License

Artistic-2.0

Maintainer

Heidi Dvinge

Last Published

February 15th, 2017

Functions in HTqPCR (1.26.0)

plotCtPairs

Pairwise scatterplot of multiple sets of Ct values from qPCR data.
plotCtOverview

Overview plot of qPCR Ct values across multiple conditions.
cbind

Combine qPCRset objects
readCtData

Reading Ct values from qPCR experiments data into a qPCRset
HTqPCR-package

Analysis of High-Throughput qPCR data (HTqPCR)
heatmapSig

Heatmap of deltadeltaCt values from qPCR data.
plotCVBoxes

Boxplots of CV for qPCR Ct values.
plotCtCard

Image plot of qPCR Ct values from a card format
plotCtLines

Plotting Ct values from qPCR across multiple samples.
plotCtPCA

PCA for qPCR Ct values.
plotCtVariation

Plot variation in Ct values across replicates
filterCategory

Filter Ct values based on their feature categories.
mannwhitneyCtData

Differentially expressed features with qPCR: Mann-Whitney
plotCtHistogram

Histrogram of Ct values from qPCR experiments.
ttestCtData

Differentially expressed features with qPCR: t-test
plotCtScatter

Scatterplot of two sets of Ct values from qPCR data.
setCategory

Assign categories to Ct values from qPCR data.
plotCtDensity

Distribution plot for qPCR Ct values.
qPCRraw

Example raw qPCR data.
plotCtSignificance

Barplot with Ct values between genes from qPCR.
filterCtData

Filter out features (genes) from qPCR data.
qPCRset-class

Class "qPCRset"
clusterCt

Clustering of qPCR Ct values
qPCRpros

Example processed qPCR data
plotCtReps

Scatter plot of features analysed twice during each qPCR experiment.
limmaCtData

Differentially expressed features with qPCR: limma
changeCtLayout

Changing the dimensions (rows x columns) of qPCRset objects
plotCtCor

Correlation between Ct values from qPCR data
plotCtArray

Image plot of qPCR Ct values from an array format
plotCtCategory

Summarising the feature categories for Ct values.
plotCtBoxes

Boxplots for qPCR Ct values.
normalizeCtData

Normalization of Ct values from qPCR data.
plotCtRQ

Plot the relative quantification of Ct values from qPCR experiments.
plotCtHeatmap

Heatmap of qPCR Ct values.