HTqPCR

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of HTqPCR; for the stable release version, see HTqPCR.

Automated analysis of high-throughput qPCR data

Bioconductor version: Development (3.21)

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: Matthew N. McCall <mccallm at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DifferentialExpression, GeneExpression, MicrotitrePlateAssay, MultipleComparison, Preprocessing, QualityControl, Software, Visualization, qPCR
Version	1.61.2
In Bioconductor since	BioC 2.5 (R-2.10) (15.5 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

Suggests	statmod
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

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

Source Package	HTqPCR_1.61.2.tar.gz
Windows Binary (x86_64)	HTqPCR_1.61.2.zip
macOS Binary (x86_64)	HTqPCR_1.61.2.tgz
macOS Binary (arm64)	HTqPCR_1.61.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HTqPCR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HTqPCR
Package Short Url	https://bioconductor.org/packages/HTqPCR/
Package Downloads Report	Download Stats