HTqPCR: Automated analysis of high-throughput qPCR data

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
Date of publicationNone
MaintainerHeidi Dvinge <hdvinge@fredhutch.org>
LicenseArtistic-2.0
Version1.28.0
http://www.ebi.ac.uk/bertone/software

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

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