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HTqPCR

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

Automated analysis of high-throughput qPCR data

Bioconductor version: Development (3.18)

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")

# 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
NEWS Text

Details

biocViews DataImport, DifferentialExpression, GeneExpression, MicrotitrePlateAssay, MultipleComparison, Preprocessing, QualityControl, Software, Visualization, qPCR
Version 1.55.0
In Bioconductor since BioC 2.5 (R-2.10) (14 years)
License Artistic-2.0
Depends Biobase, RColorBrewer, limma
Imports affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils
Linking To
Suggests statmod
System Requirements
Enhances
URL http://www.ebi.ac.uk/bertone/software
See More
Depends On Me
Imports Me nondetects, unifiedWMWqPCR
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package HTqPCR_1.55.0.tar.gz
Windows Binary HTqPCR_1.55.0.zip (64-bit only)
macOS Binary (x86_64) HTqPCR_1.55.0.tgz
macOS Binary (arm64) HTqPCR_1.55.0.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