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).
|Author||Heidi Dvinge, Paul Bertone|
|Date of publication||None|
|Maintainer||Heidi Dvinge <firstname.lastname@example.org>|
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