Last data update: 2014.03.03
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chipPCR
Package: chipPCR
Type: Package
Title: Toolkit of Helper Functions to Pre-Process Amplification Data
Version: 0.0.8-10
LazyData: true
Date: 2015-04-08
Authors@R: c(
person("Stefan", "Roediger",
email = "stefan.roediger@hs-lausitz.de",
role = c("cre", "aut")),
person("Michal", "Burdukiewicz",
email = "michalburdukiewicz@gmail.com", role = "aut"),
person("Konstantin A.", "Blagodatskikh",
email = "k.blag@yandex.ru", role = "ctb"))
Description: 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.
License: GPL-3
URL: https://github.com/michbur/chipPCR
BugReports: https://github.com/michbur/chipPCR/issues
Depends: R (>= 3.0.0), methods
Suggests: drc, knitr, markdown, MBmca (>= 0.0.3-4), qpcR, RDML, xtable
VignetteBuilder: knitr
Imports: lmtest, MASS, outliers, ptw, quantreg, Rfit, robustbase,
shiny, signal
Packaged: 2015-04-09 18:11:32 UTC; tux
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-10 01:10:56
Author: Stefan Roediger [cre, aut],
Michal Burdukiewicz [aut],
Konstantin A. Blagodatskikh [ctb]
Maintainer: Stefan Roediger <stefan.roediger@hs-lausitz.de>
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'chipPCR' ...
** package 'chipPCR' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'qqnorm' from package 'stats' in package 'chipPCR'
Creating a generic function for 'qqline' from package 'stats' in package 'chipPCR'
** help
*** installing help indices
converting help for package 'chipPCR'
finding HTML links ... done
AmpSim html
AmpSim.gui html
C126EG595 html
C126EG685 html
C127EGHP html
C17 html
C316.amp html
C316.melt.hr html
C316.melt.lr html
C317.amp html
C317.melt.hr html
C317.melt.lr html
C54 html
C60.amp html
C60.melt html
C67 html
C81 html
C85 html
CD74 html
CD75 html
CPP html
Eff1000 html
Eff625 html
Eff750 html
Eff875 html
LAMP html
MFIaggr html
MFIaggr.gui html
RPA html
VIMCFX96_60 html
VIMCFX96_69 html
VIMCFX96_meltcurve html
VIMiQ5_595 html
VIMiQ5_685 html
VIMiQ5_melt html
amptest-class html
amptester html
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/amptester.Rd:45: missing file link 'tail'
amptester.gui html
bg-class html
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/bg-class.Rd:29: missing file link 'plot.bg'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/bg-class.Rd:34: missing file link 'summary.bg'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/bg-class.Rd:44: missing file link 'plot.bg'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/bg-class.Rd:45: missing file link 'summary.bg'
bg.max html
capillaryPCR html
chipPCR-package html
chipPCR.datasets html
der-class html
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/der-class.Rd:24: missing file link 'summary.der'
eff-class html
effcalc html
fixNA html
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/fixNA.Rd:35: missing file link 'spline'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/fixNA.Rd:36: missing file link 'approx'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/fixNA.Rd:54: missing file link 'approx'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/fixNA.Rd:57: missing file link 'spline'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/fixNA.Rd:74: missing file link 'approx'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/fixNA.Rd:74: missing file link 'spline'
humanrater html
inder html
lm.coefs html
normalizer html
plot-bg html
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/plot-bg.Rd:56: missing file link 'plot.der'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/plot-bg.Rd:65: missing file link 'plot.der'
plot-der html
plot-eff html
plot-refMFI html
plotCurves html
refMFI-class html
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/refMFI-class.Rd:38: missing file link 'qqline'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/refMFI-class.Rd:40: missing file link 'plot.refMFI'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/refMFI-class.Rd:47: missing file link 'summary.refMFI'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/refMFI-class.Rd:60: missing file link 'plot.refMFI'
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/refMFI-class.Rd:61: missing file link 'summary.refMFI'
rounder html
smoother html
summary-bg html
Rd warning: /tmp/RtmpZPeizR/R.INSTALL55eab2c6b06/chipPCR/man/summary-bg.Rd:10: missing file link 'bg'
summary-der html
summary-refMFI html
th-class html
th.cyc html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chipPCR)
Making 'packages.html' ... done
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