HTqPCR

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see HTqPCR.

Automated analysis of high-throughput qPCR data

Bioconductor version: 3.7

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 "3.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DifferentialExpression, GeneExpression, MicrotitrePlateAssay, MultipleComparison, Preprocessing, QualityControl, Software, Visualization, qPCR
Version	1.34.0
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

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_1.34.0.tar.gz
Windows Binary	HTqPCR_1.34.0.zip
Mac OS X 10.11 (El Capitan)	HTqPCR_1.34.0.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
Old Source Packages for BioC 3.7	Source Archive