chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data
Version 0.0.8-10

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.

Package details

AuthorStefan Roediger [cre, aut], Michal Burdukiewicz [aut], Konstantin A. Blagodatskikh [ctb]
Date of publication2015-04-10 01:10:56
MaintainerStefan Roediger <stefan.roediger@hs-lausitz.de>
LicenseGPL-3
Version0.0.8-10
URL https://github.com/michbur/chipPCR
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("chipPCR")

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chipPCR documentation built on May 29, 2017, 6:46 p.m.