PCRedux

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) <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 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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Description file content

Package
PCRedux
Type
Package
Title
Quantitative Polymerase Chain Reaction (qPCR) Data Mining and Machine Learning Helper Tool
Version
0.2.6-1
Date
2018-01-23
Description
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.
License
MIT + file LICENSE
LazyLoad
yes
LazyData
yes
URL
BugReports
https://github.com/devSJR/PCRedux/issues
Depends
R (>= 3.3.0)
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
NeedsCompilation
no
VignetteBuilder
knitr
RoxygenNote
6.0.1
Packaged
2018-06-13 13:58:41 UTC; tux
Author
Stefan Roediger [cre, aut], Michal Burdukiewicz [aut], Andrej-Nikolai Spiess [aut], Konstantin A. Blagodatskikh [aut]
Maintainer
Stefan Roediger
Repository
CRAN
Date/Publication
2018-06-13 21:38:05 UTC

install.packages('PCRedux')

0.2.6-1

3 months ago

https://github.com/devSJR/PCRedux

Stefan Roediger

MIT + file LICENSE

Depends on

R (>= 3.3.0)

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

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