R Observatory: Metrics for dpcR version 0.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

dpcR

0.6Package record

Digital PCR Analysis

0packages depend

2.7Kdownloads / year

–test coverage

8/13flavors OK

Overview

About

Maintained by Andrej-Nikolai SpiessCRAN page ↗GitHub ↗Issues ↗

Analysis, visualisation and simulation of digital polymerase chain reaction (dPCR) (Burdukiewicz et al. (2016) doi:10.1016/j.bdq.2016.06.004). Supports data formats of commercial systems (Bio-Rad QX100 and QX200; Fluidigm BioMark) and other systems.

Install

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

install.packages("dpcR", 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("michbur/dpcR")

Development version from michbur/dpcR. 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-dpcr

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-dpcR

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

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

Health

CRAN checks

5NOTE8OK

Check messages

NOTER code for possible problemsr-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

Found calls to structure() using deprecated special names:
  dpcR/R/limit_cq.R (.Names: 1)
'.Names' should be changed to 'names'.

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘plot.qdpcr.Rd’ ‘qpcr_analyser.Rd’ ‘show-methods.Rd’
  ‘summary-methods.Rd’ ‘test_peaks.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 4.0 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.6

READMEYes · 28 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · computed when R runs itWebsitenot declared in DESCRIPTION

Help pages: 54includes a package overview page
Examples that run: 98%39 run in a plain check · 1 hold no code
Exported functions with examples: 68%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 33%

Vignettes (1)

dpcR package - an overview

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #13,126 · ~7/day · ~226/mo

Releases R versions

Daily download trend is not available in this view yet.

40630 days

86290 days

2.7K1 year

Compare downloads with other packages →

Also on79 r2u

How downloads are counted

Repository

michbur/dpcr ↗Account: michbur

9Stars

3Forks

0Open issues

0Open PRs

2Releases

608Commits

5Commit identities

608 commits · Last activity 2022-11-07 · The default branch showed an older version (0.5.1-1) than CRAN on 2026-10-11

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 18
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

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

Checks run against github.com/michbur/dpcr on 2026-10-11.

Continuous integration (1)

Travis CI (config file)

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Installing dpcR adds 91 packages (53 with compiled code, 75 MB of source tarballs). Heaviest: TH.data 8.2 MB, bslib 5.6 MB, qpcR 4.1 MB.

Depends (2)

R >= 3.0.0methods

Imports (14)

binom chipPCR e1071 evd dgof multcomp qpcR pracma rateratio.test readxl signal shiny spatstat.explore spatstat.geom

LinkingTo (0)

none

Suggests (9)

digest DT ggplot2 knitr markdown rhandsontable rmarkdown shinythemes xtable

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Andrej-Nikolai Spiess

Maintainer since 0.6 (2025), Contributor · added in 0.5

Michal Burdukiewicz

Author

Bart Jacobs

Author · added in 0.1.4.0

Stefan Roediger

Author

Piotr Sobczyk

Contributor · added in 0.1.4.0

Previously maintained by Michal Burdukiewicz (0.1.0 to 0.5).

Releases (13)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-06-18
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
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-04-09
check problems were not corrected despite reminders
R
R 3.6.0 released · 2019-04-26
unarchivedReturned to CRAN
2019-02-04
archivedRemoved from CRAN
2018-08-13
check problems were not corrected despite reminders
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

Show 15 earlier eventsHide 15 earlier events

R
R 3.1.0 released · 2014-04-10
3.0.2Latest
record
2013-09-07 · current release · diff ↗ ·
added 7 exports
sim_ddpcr, plot_vic_fam, sim_adpcr, extract_dpcr, plot_panel, dpcr_density, dpcr_density_gui
0.6
record
2025-06-18 · diff ↗
0.5
record
2019-02-04 · diff ↗
0.4
record
2017-01-03 · diff ↗ ·
removed 4 exports
analyze_pooled, read_raw, sim_ddpcr, test_ratio

added 9 exports
ddpcRquant, df2dpcr, dpcr2df, extract_run, read_QX200, read_amp, read_redf, sim_dpcr, test_pooled
0.3
record
2016-03-15 · diff ↗ ·
added 1 export
analyze_pooled
0.2
record
2015-12-11 · diff ↗ ·
added 9 exports
adpcr2panel, calc_coordinates, dpcReport, dpcr_density_table, read_BioMark, read_QX100, read_dpcr, read_raw, rename_dpcr
0.1.4.0
record
2015-04-09 · diff ↗
0.1.3.3
record
2015-02-24 · diff ↗
0.1.3.2
record
2014-12-24 · diff ↗ ·
added 2 exports
binarize, test_counts_gui
0.1.3.1
record
2014-10-07 · diff ↗ ·
added 6 exports
bind_dpcr, moments, num2int, test_counts, test_peaks, test_ratio
0.1.2-1
record
2014-07-02 · diff ↗
0.1.2
record
2014-06-30 · diff ↗ ·
added 8 exports
adpcr2ppp, bioamp, compare_dens, create_dpcr, limit_cq, qpcr2pp, qpcr_analyser, test_panel
0.1.0
record
2013-09-08
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-09-07
Total releases: 13 / 13 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.0
Bundled data: 232 KB / 7 files
Download size: 759 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("dpcR")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 dpcR version 0.6 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →