PCRedux: Quantitative Polymerase Chain Reaction (qPCR) Data Mining and Machine Learning Toolkit

Extracts features from amplification curve data of quantitative Polymerase Chain Reactions (qPCR) (Pabinger S. et al. (2014) <doi:10.1016/j.bdq.2014.08.002>) for machine learning purposes. Helper functions prepare the amplification curve data for processing as functional data (e.g., Hausdorff distance) or enable the plotting of amplification curve classes (negative, ambiguous, positive). The hookreg() and hookregNL() functions (Burdukiewicz M. et al. (2018) <doi:10.1016/j.bdq.2018.08.001>) can be used to predict amplification curves with an hook effect-like curvature. The pcrfit_single() function can be used to extract features from an amplification curve.

Version: 1.0-6
Depends: R (≥ 3.5.0)
Imports: bcp, changepoint, chipPCR, ecp, fda.usc, MBmca, pbapply, pracma, qpcR, robustbase, shiny, stats, utils, zoo
Suggests: DT, FFTrees, knitr, RDML, randomForest, readxl, rmarkdown, spelling, testthat, xtable, future, listenv
Published: 2020-03-06
Author: Stefan Roediger ORCID iD [cre, aut], Michal Burdukiewicz ORCID iD [aut], Andrej-Nikolai Spiess [aut], Konstantin A. Blagodatskikh [aut], Dominik Rafacz [ctb]
Maintainer: Stefan Roediger <stefan.roediger at b-tu.de>
BugReports: https://github.com/PCRuniversum/PCRedux/issues
License: MIT + file LICENSE
URL: https://CRAN.R-project.org/package=PCRedux
NeedsCompilation: no
Language: en-US
Materials: README NEWS ChangeLog
CRAN checks: PCRedux results


Reference manual: PCRedux.pdf
Vignettes: PCRedux package - an overview
Algorithms for Automatized Detection of Hook Effect-bearing Amplification Curves
Package source: PCRedux_1.0-6.tar.gz
Windows binaries: r-devel: PCRedux_1.0-6.zip, r-release: PCRedux_1.0-6.zip, r-oldrel: PCRedux_1.0-6.zip
macOS binaries: r-release: PCRedux_1.0-6.tgz, r-oldrel: PCRedux_1.0-6.tgz
Old sources: PCRedux archive


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