Package: chipPCR 1.0

Stefan Roediger

chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data

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. For more information see: Roediger et al. (2015) <doi:10.1093/bioinformatics/btv205>.

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

chipPCR_1.0.tar.gz
chipPCR_1.0.zip(r-4.5)chipPCR_1.0.zip(r-4.4)chipPCR_1.0.zip(r-4.3)
chipPCR_1.0.tgz(r-4.4-any)chipPCR_1.0.tgz(r-4.3-any)
chipPCR_1.0.tar.gz(r-4.5-noble)chipPCR_1.0.tar.gz(r-4.4-noble)
chipPCR_1.0.tgz(r-4.4-emscripten)chipPCR_1.0.tgz(r-4.3-emscripten)
chipPCR.pdf |chipPCR.html✨
chipPCR/json (API)

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

Peer review:

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

Datasets:
  • C126EG595 - QPCR Experiment for the Amplification of HPRT1 Using the Bio-Rad iQ5 thermo cycler
  • C126EG685 - QPCR Experiment for the Amplification of HPRT1 Using the Roche Light Cycler 1.5
  • C127EGHP - QPCR Experiment for the Amplification of MLC-2v Using the Roche Light Cycler 1.5
  • C17 - Helicase Dependent Amplification of HPRT1 at Different Temperatures using the 'VideoScan' Platform 2.0
  • C316.amp - QPCR Experiment for the Amplification of adk Using the Bio-Rad iQ5 thermo cycler
  • C316.melt.hr - Melting Curves (resolution: 0.2 degrees Celsius / step) for the Gene adk Using the Bio-Rad iQ5 thermo cycler
  • C316.melt.lr - Melting Curves (resolution: 0.5 degrees Celsius / step) for the Gene adk Using the Bio-Rad iQ5 thermo cycler
  • C317.amp - QPCR Experiment for the Amplification of adk Using the Bio-Rad CFX96 thermo cycler
  • C317.melt.hr - Melting Curves (resolution: 0.1 degrees Celsius / step) for the Gene adk Using the Bio-Rad CFX96 thermo cycler
  • C317.melt.lr - Melting Curves (resolution: 0.5 degrees Celsius / step) for the Gene adk Using the Bio-Rad CFX96 thermo cycler
  • C54 - QPCR Experiment for the amplification of MLC-2v using the 'VideoScan' heating/cooling-unit
  • C60.amp - QPCR Experiment for the Amplification of MLC-2v and Vimentin (as decadic dilutions) Using the Roche Light Cycler 1.5
  • C60.melt - Melt Curves MLC-2v and Vimentin for the qPCR Experiment C60.amp Using the Roche Light Cycler 1.5
  • C67 - Helicase Dependent Amplification of HPRT1 with different input DNA quantities using the Bio-Rad iQ5 thermo cycler
  • C81 - Helicase Dependent Amplification of pCNG1 using the 'VideoScan' Platform
  • C85 - Helicase Dependent Amplification of Vimentin using the 'VideoScan' Platform
  • CD74 - Quantitative PCR with a hydrolysis probe and DNA binding dye
  • CD75 - Helicase Dependent Amplification in the 'VideoScan' 'HCU'
  • Eff1000 - Highly Replicate Number Amplification Curves
  • Eff625 - Highly Replicate Number Amplification Curves
  • Eff750 - Highly Replicate Number Amplification Curves
  • Eff875 - Highly Replicate Number Amplification Curves
  • LAMP - Real-time loop-mediated isothermal amplification
  • RPA - Recombinase polymerase amplification
  • VIMCFX96_60 - Amplification Reaction Using the Bio-Rad CFX96
  • VIMCFX96_69 - Amplification Reaction Using the Bio-Rad CFX96
  • VIMCFX96_meltcurve - Melting Curve Measured with the Bio-Rad CFX96
  • VIMiQ5_595 - Amplification Reaction Using the Bio-Rad iQ5
  • VIMiQ5_685 - Amplification Reaction Using the Bio-Rad iQ5
  • VIMiQ5_melt - Melting Curve Measured with the Bio-Rad iQ5
  • capillaryPCR - Capillary convective PCR

On CRAN:

23 exports 8 stars 2.16 score 47 dependencies 1 dependents 3 mentions 99 scripts 1.4k downloads

Last updated 4 years agofrom:b7c751a871. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 31 2024
R-4.5-winNOTEAug 31 2024
R-4.5-linuxNOTEAug 31 2024
R-4.4-winNOTEAug 31 2024
R-4.4-macNOTEAug 31 2024
R-4.3-winOKAug 31 2024
R-4.3-macOKAug 31 2024

Exports:AmpSimAmpSim.guiamptesteramptester.guibg.maxCPPeffcalcfixNAhumanraterinderlm.coefsMFIaggrMFIaggr.guinormalizerplotplotCurvesqqlineqqnormroundershowsmoothersummaryth.cyc

Dependencies:base64encbslibcachemclicommonmarkcrayonDEoptimRdigestfastmapfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclelmtestmagrittrMASSMatrixMatrixModelsmemoisemimeoutlierspromisesptwquantregR6rappdirsRcppRcppArmadilloRcppDERfitrlangrobustbasesassshinysignalsourcetoolsSparseMsurvivalwithrxtablezoo

Supplement to: chipPCR: an R Package to Pre-Process Raw Data of Amplification Curves

The chipPCR package authors

Rendered fromchipPCR.Rmdusingknitr::rmarkdownon Aug 31 2024.

Last update: 2021-02-26
Started: 2020-12-13

Readme and manuals

Help Manual

Help pageTopics
Toolkit of functions to pre-process amplification datachipPCR-package chipPCR
Amplification curve simulatorAmpSim
Amplification Curve Simulation Graphical User InterfaceAmpSim.gui
Class '"amptest"'amptest amptest-class plot,amptest,ANY-method plot,amptest-method plot.amptest show,amptest-method show.amptest summary,amptest-method summary.amptest
Amplification testamptester
Amplification Test Graphical User Interfaceamptester.gui
Class '"bg"'bg bg-class show,bg-method show.bg
Simple function to detect and correct the background rangebg.max bg.max,data.frame,missing-method bg.max,matrix,missing-method bg.max,numeric,numeric-method bg.max.data.frame bg.max.matrix bg.max.numeric
qPCR Experiment for the Amplification of HPRT1 Using the Bio-Rad iQ5 thermo cyclerC126EG595
qPCR Experiment for the Amplification of HPRT1 Using the Roche Light Cycler 1.5C126EG685
qPCR Experiment for the Amplification of MLC-2v Using the Roche Light Cycler 1.5C127EGHP
Helicase Dependent Amplification of HPRT1 at Different Temperatures using the 'VideoScan' Platform 2.0C17
qPCR Experiment for the Amplification of adk Using the Bio-Rad iQ5 thermo cyclerC316.amp
Melting Curves (resolution: 0.2 degrees Celsius / step) for the Gene adk Using the Bio-Rad iQ5 thermo cyclerC316.melt.hr
Melting Curves (resolution: 0.5 degrees Celsius / step) for the Gene adk Using the Bio-Rad iQ5 thermo cyclerC316.melt.lr
qPCR Experiment for the Amplification of adk Using the Bio-Rad CFX96 thermo cyclerC317.amp
Melting Curves (resolution: 0.1 degrees Celsius / step) for the Gene adk Using the Bio-Rad CFX96 thermo cyclerC317.melt.hr
Melting Curves (resolution: 0.5 degrees Celsius / step) for the Gene adk Using the Bio-Rad CFX96 thermo cyclerC317.melt.lr
qPCR Experiment for the amplification of MLC-2v using the 'VideoScan' heating/cooling-unitC54
qPCR Experiment for the Amplification of MLC-2v and Vimentin (as decadic dilutions) Using the Roche Light Cycler 1.5C60.amp
Melt Curves MLC-2v and Vimentin for the qPCR Experiment C60.amp Using the Roche Light Cycler 1.5C60.melt
Helicase Dependent Amplification of HPRT1 with different input DNA quantities using the Bio-Rad iQ5 thermo cyclerC67
Helicase Dependent Amplification of pCNG1 using the 'VideoScan' PlatformC81
Helicase Dependent Amplification of Vimentin using the 'VideoScan' PlatformC85
capillary convective PCRcapillaryPCR
Quantitative PCR with a hydrolysis probe and DNA binding dyeCD74
Helicase Dependent Amplification in the 'VideoScan' 'HCU'CD75
Overview for data sets of the 'chipPCR' packagechipPCR.datasets
Curve Pre-processorCPP CPP,data.frame,missing-method CPP,matrix,missing-method CPP,numeric,numeric-method CPP.data.frame CPP.matrix CPP.numeric
Class '"der"'der der-class show,der-method show.der
Class '"eff"'eff eff-class show,eff-method show.eff summary,eff-method summary.eff
Highly Replicate Number Amplification CurvesEff1000
Highly Replicate Number Amplification CurvesEff625
Highly Replicate Number Amplification CurvesEff750
Highly Replicate Number Amplification CurvesEff875
Analysis of the amplification efficiencyeffcalc effcalc,data.frame,missing-method effcalc,matrix,missing-method effcalc,numeric,numeric-method effcalc.data.frame effcalc.matrix effcalc.numeric
Impute missing values into a column of amplification datafixNA fixNA,data.frame,missing-method fixNA,matrix,missing-method fixNA,numeric,numeric-method fixNA.data.frame fixNA.matrix fixNA.numeric
humanrater, a graphical interface to rate curveshumanrater
Interpolate derivativesinder inder,data.frame,missing-method inder,matrix,missing-method inder,numeric,numeric-method inder.data.frame inder.matrix inder.numeric
real-time loop-mediated isothermal amplification (LAMP) by Tanner et al. (2012)LAMP
Compute linear model coefficientslm.coefs
Multiple comparison of the cycle dependent variance of the fluorescenceMFIaggr MFIaggr,data.frame,missing-method MFIaggr,matrix,missing-method MFIaggr,numeric,numeric-method MFIaggr.data.frame MFIaggr.matrix MFIaggr.numeric
Multiple Comparison of the Cycle Dependent Variance - Graphical User InterfaceMFIaggr.gui
Normalize datanormalizer
Plot 'bg' objectsplot,bg,ANY-method plot,bg-method plot.bg
Plot 'der' objectsplot,der,ANY-method plot,der-method plot.der
Plot 'eff' objectsplot,eff,ANY-method plot,eff-method plot.eff
Plot 'refMFI' objectsplot,refMFI,ANY-method plot,refMFI,refMFI-method plot,refMFI-method plot.refMFI
Plot Curves in an Orthogonal MatrixplotCurves
Class '"refMFI"'qqline,refMFI-method qqnorm,refMFI-method refMFI refMFI-class show,refMFI-method
Round der objectsrounder
Recombinase polymerase amplification (RPA) by Lutz et al.(2009)RPA
Wrapper for Several Smoothers of Amplification Datasmoother smoother,data.frame,missing-method smoother,matrix,missing-method smoother,numeric,numeric-method smoother.data.frame smoother.matrix smoother.numeric
Summary 'bg' objectssummary,bg-method summary.bg
Summary 'der' objectssummary,der-method summary-der summary.der
Summary 'refMFI' objectssummary,refMFI-method summary.refMFI
Class '"th"'show,th-method show.th summary,th-method summary.th th th-class
Threshold Cycleth.cyc
Amplification Reaction Using the Bio-Rad CFX96VIMCFX96_60
Amplification Reaction Using the Bio-Rad CFX96VIMCFX96_69
Melting Curve Measured with the Bio-Rad CFX96VIMCFX96_meltcurve
Amplification Reaction Using the Bio-Rad iQ5VIMiQ5_595
Amplification Reaction Using the Bio-Rad iQ5VIMiQ5_685
Melting Curve Measured with the Bio-Rad iQ5VIMiQ5_melt