chipPCR

Toolkit of Helper Functions to Pre-Process Amplification Data

v1.0-2 · Mar 4, 2021 · GPL-3

Description

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>.

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r-devel-linux-x86_64-debian-clang	NOTE	144.6s
r-devel-linux-x86_64-debian-gcc	NOTE	99.3s
r-devel-linux-x86_64-fedora-clang	NOTE	215s
r-devel-linux-x86_64-fedora-gcc	NOTE	234.6s
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r-devel-windows-x86_64	NOTE	178s
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r-oldrel-windows-x86_64	NOTE	217s
r-patched-linux-x86_64	NOTE	135.7s
r-release-linux-x86_64	NOTE	133.7s
r-release-macos-arm64	NOTE
r-release-macos-x86_64	NOTE	145s
r-release-windows-x86_64	NOTE	172s

Check details (16 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Stefan Roediger <stefan.roediger@b-tu.de>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

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NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Stefan Roediger <stefan.roediger@b-tu.de>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

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Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Stefan Roediger <stefan.roediger@b-tu.de>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Stefan Roediger <stefan.roediger@b-tu.de>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-fedora-clang

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Reverse Dependencies (4)

imports

MBmca PCRedux dpcR

suggests

RDML

Dependency Network

Version History

new 1.0-2 Mar 9, 2026

Maintainer

Stefan Roediger

Dependencies

Depends

R (>= 3.0.0) methods

Imports

lmtest MASS outliers ptw quantreg Rfit robustbase shiny signal

Suggests

drc knitr markdown qpcR RDML rmarkdown spelling testthat tinytex xtable

Compilation

No compilation needed

First Published

Mar 9, 2026

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