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HTqPCR

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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HTqPCR")

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

Documentation

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

browseVignettes("HTqPCR")
qPCR analysis in R PDF R Script
Reference Manual PDF
NEWS Text

Details

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
See More
Suggests statmod
Linking To
Enhances
Depends On Me
Imports Me nondetects, unifiedWMWqPCR
Suggests Me
Links To Me
Build Report Build Report

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/
Package Downloads Report Download Stats