Package: qpcR 1.4-2

qpcR: Modelling and Analysis of Real-Time PCR Data

Sigmoidal model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR), according to Ritz & Spiess (2008) <doi:10.1093/bioinformatics/btn227> and Spiess et al. (2008) <doi:10.1186/1471-2105-9-221>.

Authors:Andrej-Nikolai Spiess [aut, cre]

qpcR_1.4-2.tar.gz
qpcR_1.4-2.zip(r-4.7)qpcR_1.4-2.zip(r-4.6)qpcR_1.4-2.zip(r-4.5)
qpcR_1.4-2.tgz(r-4.6-x86_64)qpcR_1.4-2.tgz(r-4.6-arm64)qpcR_1.4-2.tgz(r-4.5-x86_64)qpcR_1.4-2.tgz(r-4.5-arm64)
qpcR_1.4-2.tar.gz(r-4.7-arm64)qpcR_1.4-2.tar.gz(r-4.7-x86_64)qpcR_1.4-2.tar.gz(r-4.6-arm64)qpcR_1.4-2.tar.gz(r-4.6-x86_64)
qpcR_1.4-2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
qpcR/json (API)
NEWS

# Install 'qpcR' in R:
install.packages('qpcR', repos = c('https://anspiess.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • b4 - The nonlinear/mechanistic models implemented in qpcR
  • b5 - The nonlinear/mechanistic models implemented in qpcR
  • b6 - The nonlinear/mechanistic models implemented in qpcR
  • b7 - The nonlinear/mechanistic models implemented in qpcR
  • batsch1 - The (published) datasets implemented in qpcR
  • batsch2 - The (published) datasets implemented in qpcR
  • batsch3 - The (published) datasets implemented in qpcR
  • batsch4 - The (published) datasets implemented in qpcR
  • batsch5 - The (published) datasets implemented in qpcR
  • boggy - The (published) datasets implemented in qpcR
  • cm3 - The nonlinear/mechanistic models implemented in qpcR
  • competimer - The (published) datasets implemented in qpcR
  • dil4reps94 - The (published) datasets implemented in qpcR
  • dyemelt - The (published) datasets implemented in qpcR
  • expGrowth - The nonlinear/mechanistic models implemented in qpcR
  • expSDM - The nonlinear/mechanistic models implemented in qpcR
  • guescini1 - The (published) datasets implemented in qpcR
  • guescini2 - The (published) datasets implemented in qpcR
  • htPCR - The (published) datasets implemented in qpcR
  • karlen1 - The (published) datasets implemented in qpcR
  • karlen2 - The (published) datasets implemented in qpcR
  • karlen3 - The (published) datasets implemented in qpcR
  • l4 - The nonlinear/mechanistic models implemented in qpcR
  • l5 - The nonlinear/mechanistic models implemented in qpcR
  • l6 - The nonlinear/mechanistic models implemented in qpcR
  • l7 - The nonlinear/mechanistic models implemented in qpcR
  • lievens1 - The (published) datasets implemented in qpcR
  • lievens2 - The (published) datasets implemented in qpcR
  • lievens3 - The (published) datasets implemented in qpcR
  • lin2 - The nonlinear/mechanistic models implemented in qpcR
  • linexp - The nonlinear/mechanistic models implemented in qpcR
  • mak2 - The nonlinear/mechanistic models implemented in qpcR
  • mak2i - The nonlinear/mechanistic models implemented in qpcR
  • mak3 - The nonlinear/mechanistic models implemented in qpcR
  • mak3i - The nonlinear/mechanistic models implemented in qpcR
  • reps - The (published) datasets implemented in qpcR
  • reps2 - The (published) datasets implemented in qpcR
  • reps3 - The (published) datasets implemented in qpcR
  • reps384 - The (published) datasets implemented in qpcR
  • rutledge - The (published) datasets implemented in qpcR
  • spl3 - The nonlinear/mechanistic models implemented in qpcR
  • testdat - The (published) datasets implemented in qpcR
  • vermeulen1 - The (published) datasets implemented in qpcR
  • vermeulen2 - The (published) datasets implemented in qpcR

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

5.52 score 2 stars 2 packages 1.1k scripts 2.6k downloads 73 mentions 44 exports 34 dependencies

Last updated from:0ad07f2036. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK229
linux-devel-x86_64OK201
source / vignettesOK189
linux-release-arm64OK222
linux-release-x86_64OK187
macos-release-arm64OK149
macos-release-x86_64OK227
macos-oldrel-arm64OK129
macos-oldrel-x86_64OK222
windows-develOK145
windows-releaseOK134
windows-oldrelOK117
wasm-releaseOK151

Exports:AICcakaike.weightscalibCy0effefficiencyevidenceexpcompexpfitfitchisqgetParis.outlierKODllratioLOF.testLREmaxRatiomeltcurvemidpointmodlistmselectparKODpcrbatchpcrbootpcrfitpcrGOFpcropt1pcrsimPRESSpropagateqpcR.newsratiobatchratiocalcratioParrefmeanreplistresplotresVarRMSERsqRsq.adRSSsliwintakeoff

Dependencies:base64encbslibcachemcliDEoptimRdigestevaluatefastmapfontawesomefshighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlatticelifecyclemagrittrMASSMatrixmemoisemimeminpack.lmR6rappdirsrglrlangrmarkdownrobustbasesasstinytexxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Akaike's second-order corrected Information CriterionAICc
Calculation of Akaike weights/relative likelihoods/delta-AICsakaike.weights
Calculation of qPCR efficiency using dilution curves and replicate bootstrappingcalib
Cy0 alternative to threshold cycles as in Guescini et al. (2008)Cy0
The amplification efficiency curve of a fitted objecteff
Calculation of qPCR efficiency and other important qPCR parametersefficiency
Evidence ratio for model comparisons with AIC, AICc or BICevidence
Comparison of all sigmodal models within the exponential regionexpcomp
Calculation of PCR efficiency by fitting an exponential modelexpfit
The chi-square goodness-of-fitfitchisq
Batch calculation of qPCR fit parameters/efficiencies/threshold cycles with simple output, especially tailored to high-throughput datagetPar
Outlier summary for objects of class 'modlist' or 'replist'is.outlier
(K)inetic (O)utlier (D)etection using several methodsKOD
Calculation of likelihood ratios for nested modelsllratio
Formal lack-Of-Fit test of a nonlinear model against a one-way ANOVA modelLOF.test
Calculation of qPCR efficiency by the 'linear regression of efficiency' methodLRE
The maxRatio method as in Shain et al. (2008)maxRatio
Melting curve analysis with (iterative) Tm identification and peak area calculation/cutoffmeltcurve
Calculation of the 'midpoint' regionmidpoint
Create nonlinear models from a dataframe and coerce them into a listmodlist
Sigmoidal model selection by different criteriamselect
Parameters that can be changed to tweak the kinetic outlier methodsparKOD
Batch calculation of qPCR efficiency and other qPCR parameterspcrbatch
Bootstrapping and jackknifing qPCR datapcrboot
Workhorse function for qPCR model fittingpcrfit
Summarize measures for the goodness-of-fitpcrGOF
Combinatorial elimination of plateau and ground phase cyclespcropt1
Simulation of sigmoidal qPCR data with goodness-of-fit analysispcrsim
Plotting qPCR data with fitted curvesplot.pcrfit
Value prediction from a fitted qPCR modelpredict.pcrfit
Allen's PRESS (Prediction Sum-Of-Squares) statistic, aka P-squarePRESS
Error propagation using different methodspropagate
The (published) datasets implemented in qpcRbatsch1 batsch2 batsch3 batsch4 batsch5 boggy competimer dil4reps94 dyemelt guescini1 guescini2 htPCR karlen1 karlen2 karlen3 lievens1 lievens2 lievens3 reps reps2 reps3 reps384 rutledge testdat vermeulen1 vermeulen2
The nonlinear/mechanistic models implemented in qpcRb4 b5 b6 b7 cm3 expGrowth expSDM l4 l5 l6 l7 lin2 linexp mak2 mak2i mak3 mak3i spl3
Display news and changes of qpcR package versionsqpcR.news
Calculation of ratios in a batch format for multiple genes/samplesratiobatch
Calculation of ratios from qPCR runs with/without reference genesratiocalc
Calculation of ratios in a batch format from external PCR parametersratioPar
Averaging of multiple reference genesrefmean
Amalgamation of single data models into a model containing replicatesreplist
An (overlayed) residuals barplotresplot
Residual variance of a fitted modelresVar
Root-mean-squared-error of a fitted modelRMSE
R-square value of a fitted modelRsq
Adjusted R-square value of a fitted modelRsq.ad
Residual sum-of-squares of a fitted modelRSS
Calculation of qPCR efficiency by the 'window-of-linearity' methodsliwin
Calculation of the qPCR takeoff pointtakeoff
Updating and refitting a qPCR modelupdate.pcrfit