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Automated analysis of high-throughput qPCR data

Bioconductor version: Release (3.18)

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

Maintainer: Heidi Dvinge <hdvinge at fredhutch.org>

Citation (from within R, enter citation("HTqPCR")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

qPCR analysis in R PDF R Script
Reference Manual PDF


biocViews DataImport, DifferentialExpression, GeneExpression, MicrotitrePlateAssay, MultipleComparison, Preprocessing, QualityControl, Software, Visualization, qPCR
Version 1.56.0
In Bioconductor since BioC 2.5 (R-2.10) (14.5 years)
License Artistic-2.0
Depends Biobase, RColorBrewer, limma
Imports affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils
System Requirements
URL http://www.ebi.ac.uk/bertone/software
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Suggests statmod
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Imports Me nondetects, unifiedWMWqPCR
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HTqPCR_1.56.0.tar.gz
Windows Binary HTqPCR_1.56.0.zip
macOS Binary (x86_64) HTqPCR_1.56.0.tgz
macOS Binary (arm64) HTqPCR_1.56.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HTqPCR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HTqPCR
Bioc Package Browser https://code.bioconductor.org/browse/HTqPCR/
Package Short Url https://bioconductor.org/packages/HTqPCR/
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