chipPCR

1.0-2

Toolkit of Helper Functions to Pre-Process Amplification Data

4packages depend

12.8Kdownloads / year

0.0%test coverage

0/13checks pass

Overview

About

Maintained by Stefan RoedigerFirst published 2013-12-129 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("chipPCR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("PCRuniversum/chipPCR")

Development version from PCRuniversum/chipPCR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-chippcr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-chipPCR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-chipPCR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 4.3 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.00

0.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 189 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 94%
Return-value docs: 89%
References docs: 69%

Downloads

12.8K

CRAN downloads in the past year

Rank #4,094 · ~35/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

57330 days

2.3K90 days

12.8K1 year

Compare downloads with other packages →

Also on232 r2u11 autocran

Repository

GitHub ↗ pcruniversum/chippcr

8Stars

6Forks

3Open issues

1Open PRs

0Releases

569Commits

6Contributors

569 commits · Last activity 2021-02-27

Stars over time

2024-02-09 · 82026-07-07 · 8

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/pcruniversum/chippcr on 2026-07-19.

Continuous integration (2)

GitHub ActionsTravis CI

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.0.0methods

Imports (9)

lmtestMASSoutliers ptw quantreg Rfit robustbase shiny signal

LinkingTo (0)

none

Suggests (10)

drc knitr markdown qpcR RDML rmarkdown spelling testthat tinytex xtable

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

MBmca PCRedux dpcR RDML

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Stefan Roediger

Maintainer, Author

Authors (2)

Stefan Roediger

Maintainer, Author

Michal Burdukiewicz

Author

Contributors (2)

Konstantin A. Blagodatskikh

Contributor · added in 0.0.8-6

Andrej-Nikolai Spiess

Contributor · added in 1.0-2

Package Timeline

9 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0-2Latest
2021-03-05 · current release · diff ↗
unarchivedReturned to CRAN
2021-03-05
archivedRemoved from CRAN
2020-12-16
mail to the maintainer bounced
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
0.0.8-10
2015-04-10 · diff ↗

Show 9 earlier events

0.0.8-8
2015-03-12 · diff ↗
0.0.8-6
2015-02-23 · diff ↗
0.0.8-3
2014-09-29 · diff ↗
0.0.8-1
2014-08-26 · diff ↗
0.0.7
2014-06-25 · diff ↗
0.0.6
2014-04-24 · diff ↗
R
R 3.1.0 released · 2014-04-10
0.0.5
2013-12-12
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-12-12
Total releases: 9 / 13 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.0
Bundled data: 1.9 MB / 32 files
Download size: 2.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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