Quantitative Polymerase Chain Reaction (qPCR) Data Mining and Machine Learning Helper Tool

Extracts features from amplification curve data of quantitative Polymerase Chain Reactions (qPCR) (Pabinger, Stephan, Stefan Roediger, Albert Kriegner, Klemens Vierlinger, and Andreas Weinhauusel (2014) ) 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 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.


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Licence

PCRedux Quantitative PCR Machine Learning Helper Tool

Installation

PCRedux is presently not available on CRAN. However, you can install the latest development version of the code using the devtools R package.

# Install devtools, if you haven't already.
install.packages("devtools")
 
library(devtools)
install_github("devSJR/PCRedux")

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Reference manual

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install.packages("PCRedux")

0.2.6-1 by Stefan Roediger, 2 months ago


https://github.com/devSJR/PCRedux


Report a bug at https://github.com/devSJR/PCRedux/issues


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


Authors: Stefan Roediger [cre, aut], Michal Burdukiewicz [aut], Andrej-Nikolai Spiess [aut], Konstantin A. Blagodatskikh [aut]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports bcp, changepoint, caret, chipPCR, ecp, fda.usc, FFTrees, magrittr, MBmca, pbapply, plotly, pracma, qpcR, robustbase, randomForest, stats, testthat, utils, visdat, zoo

Suggests data.table, dplyr, knitr, RDML, readxl, rmarkdown, xtable


See at CRAN