freqpcr

0.4.0

Estimates Allele Frequency on qPCR DeltaDeltaCq from Bulk Samples

0packages depend

3Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Masaaki SudoFirst published 2025-11-081 releasesCRAN page ↗GitHub ↗

Interval estimation of the population allele frequency from qPCR analysis based on the restriction enzyme digestion (RED)-DeltaDeltaCq method (Osakabe et al. 2017, <doi:10.1016/j.pestbp.2017.04.003>), as well as general DeltaDeltaCq analysis. Compatible with the Cq measurement of DNA extracted from multiple individuals at once, so called "group-testing", this model assumes that the quantity of DNA extracted from an individual organism follows a gamma distribution. Therefore, the point estimate is robust regarding the uncertainty of the DNA yield.

Install

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

install.packages("freqpcr")

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

pak::pak("sudoms/freqpcr")

Development version from sudoms/freqpcr. Requires the pak package.

Release

# one-time r2u setup for Ubuntu (noble)

curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash

# then install

sudo apt install r-cran-freqpcr

Fast Ubuntu binaries via r2u (no compilation). Run the setup once per machine.

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

sudo dnf copr enable iucar/cran

sudo dnf install R-CRAN-freqpcr

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

sudo zypper install R-freqpcr

RPMs auto-built from CRAN on openSUSE OBS.

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

CRAN downloads in the past year

Rank #14,902 · ~8/day · ~247/mo

31230 days

74390 days

3K1 year

Also on93 r2u13 autocran

Source & community

GitHub ↗

Repository stars, issues, and contributor activity are not tracked yet.

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.6cubature

Imports (1)

methods base

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown remotes

Enhances (0)

none

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code

2,680Lines of code

5Exported functions

Code & tests

Open call graph →

Line coverage

–

Expression

–

Tests / Examples

–

Functions

11 5 exported

Complexity

6.8 avg / 31 max

Call network

11 nodes / 5 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Masaaki Sudo iD

Author, Maintainer

Release timeline

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

R
R 4.6.0 released · 2026-04-24
0.4.0Latest
2026-03-10 · current release

Package metadata

First published: 2025-11-08
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet