HTqPCR: Automated analysis of high-throughput qPCR data

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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 <hdvinge@fredhutch.org>
License
Artistic-2.0
Version
1.28.0
URLs

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

Files in this package

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