R Observatory: Metrics for chipPCR version 1.0-2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

chipPCR

1.0-2Package record

Toolkit of Helper Functions to Pre-Process Amplification Data

3packages dependsuggested by 2

9.6Kdownloads / year

0.0%test coverage

0/13flavors OK

Overview

About

Maintained by Stefan RoedigerCRAN page ↗GitHub ↗Issues ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) C316.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C317.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C60.amp.Rd:63-67: Lost braces
    63 |     40 x {
       |          ^

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

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

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

CRAN check page ↗

Slowest check: 29.8 min · r-release-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0-2

READMEYes · 189 wordsVignettesYes · 1 · staticNEWSYes · 0% structured · does not mention 1.0-2Citation fileYes · cites a publication

Help pages: 64includes a package overview page
Examples that run: 95%57 run in a plain check · 3 never run
Exported functions with examples: 94%
Documented parameters: 94%
Return-value docs: 89%
Help pages citing references: 69%

Vignettes (1)

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

How these are measured

Downloads

9.6K

CRAN downloads in the past year

Rank #5,037 · ~26/day · ~800/mo

Releases R versions

Daily download trend is not available in this view yet.

55130 days

1.7K90 days

9.6K1 year

Compare downloads with other packages →

Also on161 r2u7 autocran

How downloads are counted

Repository

pcruniversum/chippcr ↗Organization: PCRuniversum

8Stars

6Forks

3Open issues

1Open PRs

0Releases

569Commits

6Commit identities

569 commits · Last activity 2021-02-27 · The default branch showed an older version (1.0) than CRAN on 2026-10-25

Responsiveness

not measured

Stars over time

2024-02-09 · 82026-07-07 · 8

How these are measured

PracticesBeta

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

Checks run against github.com/pcruniversum/chippcr on 2026-10-25.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (2)

GitHub Pages site last deployed 2021-02-27 · The repository has a site deploy workflow

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing chipPCR adds 43 packages (29 with compiled code, 37 MB of source tarballs). Heaviest: bslib 5.6 MB, ptw 4.0 MB, promises 3.1 MB.

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

3direct

0indirect

Imports 3

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

dpcR PCRedux MBmca

Suggests, most downloaded first

RDML RDML7

How these are counted

Code & Tests

Datasets

People & History

People (4)

Stefan Roediger

Maintainer since 0.0.5 (2013), Author

Michal Burdukiewicz

Author

Konstantin A. Blagodatskikh

Contributor · added in 0.0.8-6

Andrej-Nikolai Spiess

Contributor · added in 1.0-2

Releases (9)

Pick two releases to compare their code metrics.

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
unarchivedReturned to CRAN
2021-03-05
1.0-2Latest
record
2021-03-05 · current release · diff ↗
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
record
2015-04-10 · diff ↗

Show 9 earlier eventsHide 9 earlier events

0.0.8-8
record
2015-03-12 · diff ↗
0.0.8-6
record
2015-02-23 · diff ↗
0.0.8-3
record
2014-09-29 · diff ↗
0.0.8-1
record
2014-08-26 · diff ↗ ·
added 7 exports
amptester.gui, humanrater, lm.coefs, MFIaggr.gui, normalizer, plotCurves, th.cyc
0.0.7
record
2014-06-25 · diff ↗ ·
added 4 exports
AmpSim.gui, effcalc, MFIaggr, rounder
0.0.6
record
2014-04-24 · diff ↗
R
R 3.1.0 released · 2014-04-10
0.0.5
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("chipPCR")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioinformatics/btv205.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for chipPCR version 1.0-2 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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