Package: PCRedux 1.1-2

Stefan Roediger

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. PCRedux was published in the Journal of Open Source Software (<10.21105/joss.04407>).

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

PCRedux_1.1-2.tar.gz
PCRedux_1.1-2.zip(r-4.7)PCRedux_1.1-2.zip(r-4.6)PCRedux_1.1-2.zip(r-4.5)
PCRedux_1.1-2.tgz(r-4.6-any)PCRedux_1.1-2.tgz(r-4.5-any)
PCRedux_1.1-2.tar.gz(r-4.7-any)PCRedux_1.1-2.tar.gz(r-4.6-any)
PCRedux_1.1-2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
PCRedux/json (API)

# Install 'PCRedux' in R:
install.packages('PCRedux', repos = c('https://pcruniversum.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pcruniversum/pcredux/issues

Datasets:

On CRAN:

Conda:

6.05 score 8 stars 56 scripts 276 downloads 1 mentions 16 exports 104 dependencies

Last updated from:28ed591f18. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK238
source / vignettesOK281
linux-release-x86_64OK230
macos-release-arm64OK141
macos-oldrel-arm64OK109
windows-develOK150
windows-releaseOK127
windows-oldrelOK127
wasm-releaseOK196

Exports:armorautocorrelation_testdecision_modusearlyregencuhead2tailratiohookreghookregNLhumanrater2mblrrpcrfit_singleperformeRqPCR2fdatarun_PCReduxtReemwinklR

Dependencies:ashbase64encbitopsbslibcachemchangepointchipPCRcliclustercodetoolscolorspacecommonmarkcpp11DEoptimRdeSolvedigestdoParallelecpevaluatefarverfastmapfdafda.uscfdsFNNfontawesomeforeachfsggplot2gluegtablehdrcdehighrhtmltoolshtmlwidgetshttpuvisobanditeratorsjquerylibjsonlitekernlabKernSmoothknitrkskSampleslabelinglaterlatticelifecyclelmtestlocfitmagrittrMASSMatrixMatrixModelsMBmcamclustmemoisemgcvmimeminpack.lmmulticoolmvtnormnlmeoteloutlierspbapplypcaPPpracmapromisesptwqpcRquantregR6rainbowrappdirsRColorBrewerRcppRcppArmadilloRcppDERCurlRfitrglrlangrmarkdownrobustbaseS7sassscalessegmentedshinysignalsourcetoolsSparseMSuppDistssurvivaltinytexvctrsviridisLitewithrxfunxtableyamlzoo

PCRedux package - an overview

The PCRedux package authors

Rendered fromPCRedux.Rmdusingknitr::rmarkdownon May 10 2026.

Last update: 2024-07-26
Started: 2017-08-23

Readme and manuals

Help Manual

Help pageTopics
armor: fetch errors gentlyarmor
A function to test for autocorrelation of amplification curve data from a quantitative PCR experimentautocorrelation_test
A function to get a decision (modus) from a vector of classesdecision_modus
A function to calculate the slope and intercept of an amplification curve data from a quantitative PCR experiment.earlyreg
A function to calculate numerous features from amplification curve data from a quantitative PCR experiment.encu
A function to calculate to head to tail ratio of amplification curve data from a quantitative PCR experimenthead2tailratio
A function to calculate the slope and intercept of an amplification curve data from a quantitative PCR experiment at the end of the data stream.hookreg
hookregNL - A function to calculate the slope of amplification curves in the tail regionhookregNL
Human Rater 2.0humanrater2
A function to perform a Local Robust Regression in Ranges defined by Qunantile-filteringmblrr
PCRedux - quantitative PCR Data Mining and Machine Learning ToolkitPCRedux-package PCRedux
The datasets implemented in PCReduxdata_sample decision_res_kbqPCR kbqPCR RAS002 RAS002_decisions
pcrfit_single - A function to extract features from an amplification curvepcrfit_single
Performance analysis for binary classificationperformeR
A helper function to convert amplification curve data to the fdata format.qPCR2fdata
PCRedux apprun_PCRedux
A function to Group Amplification Curves According to their ShapetReem
winklR: A function to calculate the angle based on the first and the second derivative of an amplification curve data from a quantitative PCR experiment.winklR