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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Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	152.5s
r-devel-linux-x86_64-debian-gcc	NOTE	112.5s
r-devel-linux-x86_64-fedora-clang	NOTE	269.7s
r-devel-linux-x86_64-fedora-gcc	NOTE	260.2s
r-devel-windows-x86_64	NOTE	195s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	145s
r-oldrel-windows-x86_64	NOTE	229s
r-patched-linux-x86_64	NOTE	139.6s
r-release-linux-x86_64	NOTE
r-release-macos-arm64	NOTE	40s
r-release-macos-x86_64	NOTE	141s
r-release-windows-x86_64	NOTE	181s

Check details (15 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.

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

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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.

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

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Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 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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checkRd: (-1) C316.amp.Rd:28-32: Lost braces
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NOTE r-release-linux-x86_64

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checkRd: (-1) C316.amp.Rd:28-32: Lost braces
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NOTE r-release-macos-arm64

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NOTE r-release-windows-x86_64

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checkRd: (-1) C316.amp.Rd:28-32: Lost braces
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NOTE r-oldrel-macos-arm64

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NOTE r-oldrel-windows-x86_64

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checkRd: (-1) C316.amp.Rd:28-32: Lost braces
    28 |     40 x {
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Reverse Dependencies (4)

imports

MBmca PCRedux dpcR

suggests

RDML

Dependency Network

Version History

10 tracked

new 1.0-2 Mar 10, 2026

updated 1.0-2 ← 0.0.8-10 diff Mar 4, 2021

updated 0.0.8-10 ← 0.0.8-8 diff Apr 9, 2015

updated 0.0.8-8 ← 0.0.8-6 diff Mar 11, 2015

updated 0.0.8-6 ← 0.0.8-3 diff Feb 22, 2015

updated 0.0.8-3 ← 0.0.8-1 diff Sep 28, 2014

updated 0.0.8-1 ← 0.0.7 diff Aug 25, 2014

updated 0.0.7 ← 0.0.6 diff Jun 24, 2014

updated 0.0.6 ← 0.0.5 diff Apr 23, 2014

new 0.0.5 Dec 11, 2013