Description: 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. The latest source code is available via: https://github.com/michbur/chipPCR
Imports: MASS, outliers, ptw, quantreg, Rfit, robustbase, shiny, signal

Package: chipPCR
Type: Package
Title: Toolkit of helper functions to pre-process amplification data
Version: 0.0.8-1
LazyData: true
Date: 2014-08-25
Author: Stefan Roediger, Michal Burdukiewicz
Maintainer: Stefan Roediger <stefan.roediger@hs-lausitz.de>
Description: 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. The latest source code is available via:
https://github.com/michbur/chipPCR
License: GPL-3
URL: https://github.com/michbur/chipPCR
Depends: R (>= 3.0.0), methods
Suggests: drc, knitr, markdown, MBmca (>= 0.0.3-4), qpcR, xtable
VignetteBuilder: knitr
Imports: lmtest, MASS, outliers, ptw, quantreg, Rfit, robustbase,
shiny, signal
Packaged: 2014-08-26 12:41:51 UTC; michal
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-26 15:39:23