Toolkit of Helper Functions to Pre-Process Amplification Data

A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems (VideoScan HCU, capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used.


chipPCR

The chipPCR package is a toolkit of functions to preprocess amplification curve data. Amplification data can be obtained from conventional PCR reactions or isothermal amplification reactions. The package contains functions to normalize and baseline amplification curves, a routine to detect the start of an amplification reaction, several smoothers for amplification data, a function to distinguish positive and negative amplification reactions and a function to determine the amplification efficiency. The smoothers are based on LOWESS, moving average, cubic splines, Savitzky-Golay and others.

In addition the first approximate approximate derivative maximum (FDM) and second approximate derivative maximum (SDM) can be calculated by a 5-point-stencil as quantification points from real-time amplification curves. chipPCR contains data sets of experimental nucleic acid amplification systems including the VideoScan HCU and a capillary convective PCR (ccPCR) system. The amplification data were generated by helicase dependent amplification (HDA) or polymerase chain reaction (PCR) under various temperature conditions. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used.

Installation

chipPCR is available on CRAN, so installation is as simple as:

install.packages("chipPCR")

You can install the latest development version of the code using the devtools R package.

install.packages("devtools")

library(devtools)
install_github("michbur/chipPCR")

Problems with viginette

Some distributions like Debian sid might fail to compile the package.

Messages:

sh: 1: /usr/bin/texi2dvi: not found
Calls: <Anonymous> -> texi2pdf -> texi2dvi

In this case try to install "texinfo" (apt-get install texinfo).

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("chipPCR")

0.0.8-10 by Stefan Roediger, 4 years ago


https://github.com/michbur/chipPCR


Report a bug at https://github.com/michbur/chipPCR/issues


Browse source code at https://github.com/cran/chipPCR


Authors: Stefan Roediger [cre, aut] , Michal Burdukiewicz [aut] , Konstantin A. Blagodatskikh [ctb]


Documentation:   PDF Manual  


GPL-3 license


Imports lmtest, MASS, outliers, ptw, quantreg, Rfit, robustbase, shiny, signal

Depends on methods

Suggests drc, knitr, markdown, MBmca, qpcR, RDML, xtable


Imported by PCRedux, dpcR.

Depended on by MBmca.

Suggested by RDML.


See at CRAN