rtpcr

2.1.8

qPCR Data Analysis

0packages depend

6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Ghader MirzaghaderiFirst published 2024-04-0225 releasesCRAN page ↗GitHub ↗

Tools for qPCR data analysis using Delta Ct and Delta Delta Ct methods, including t-test, Wilcoxon-test, ANOVA models, and publication-ready visualizations. The package supports multiple target, and multiple reference genes, and uses a calculation framework adopted from Ganger et al. (2017) doi:10.1186/s12859-017-1949-5 and Taylor et al. (2019) doi:10.1016/j.tibtech.2018.12.002, covering both the Livak and Pfaffl methods.

Install

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

install.packages("rtpcr", 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("mirzaghaderi/rtpcr")

Development version from mirzaghaderi/rtpcr. 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-rtpcr

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-rtpcr

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-rtpcr

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

Health

CRAN checks

13OK

Slowest check: 3.8 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-19
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-03
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 10%

Downloads

CRAN downloads in the past year

Rank #5,162 · ~16/day · ~496/mo

Releases R versions

Daily download trend is not available in this view yet.

40430 days

1.8K90 days

6K1 year

Compare downloads with other packages →

Also on565 r2u33 autocran

Repository

GitHub ↗ mirzaghaderi/rtpcr

2Stars

1Forks

1Open issues

0Open PRs

0Releases

426Commits

1Contributors

data-analysisqpcr

426 commits · Last activity 2026-07-13 · +100% stars, 30d

Stars over time

2024-06-12 · 12026-07-09 · 2

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/mirzaghaderi/rtpcr on 2026-07-19.

Docs source (1)

README.Rmd

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (11)

multcomp ggplot2 lme4 lmerTest purrr reshape2 tidyr dplyrgridemmeans lifecycle

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown multcompView

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 3,348 (56%)Rd 1,656 (27%)Vignettes 742 (12%)HTML 278 (5%)

Code characteristics

Cyclomatic complexity: 3.5 median / 37 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

18 11 exported

Complexity

8.8 avg / 37 max

Call network

18 nodes / 13 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

Datasets

Bundled datasets · 19

Name	Class	Rows × Cols	Also ships in
data_1factor	data.frame	9 × 6	–
data_1factor_Two_ref	data.frame	6 × 8	–
data_1factor_one_ref	data.frame	6 × 10	–
data_1factor_one_ref_Eff	data.frame	6 × 6	–
data_2factor	data.frame	18 × 7	–
data_2factor3ref	data.frame	24 × 11	–
data_2factorBlock	data.frame	18 × 8	–
data_2factorBlock3ref	data.frame	24 × 14	–
data_3factor	data.frame	36 × 8	–
data_Heffer2020PlosOne	data.frame	18 × 16	–
data_Lee_etal2020qPCR	data.frame	72 × 8	–
data_Yuan2006PMCBioinf	data.frame	24 × 6	–
data_efficiency1	data.frame	21 × 4	–
data_efficiency_Yuan2006PMCBioinf	data.frame	12 × 5	–
data_repeated_measure_1	data.frame	9 × 6	–
data_repeated_measure_2	data.frame	18 × 7	–
data_repeated_measure_3bLock	data.frame	18 × 10	–
data_ttest18genes	data.frame	8 × 40	–
data_withTechRep	data.frame	18 × 7	–

People & History

People (1)

Maintainer (1)

Ghader Mirzaghaderi

Author, Maintainer, Copyright holder

Authors (1)

Ghader Mirzaghaderi

Author, Maintainer, Copyright holder

Ghader Mirzaghaderi

Author, Maintainer, Copyright holder

Package Timeline

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

2.1.8Latest
2026-05-21 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.1.7
2026-04-13 · diff ↗
2.1.6
2026-03-14 · diff ↗
2.1.5
2026-02-24 · diff ↗
2.1.4
2026-02-12 · diff ↗
2.1.3
2026-02-03 · diff ↗
2.1.2
2026-01-23 · diff ↗
2.1.1
2026-01-08 · diff ↗
2.1.0
2025-12-19 · diff ↗
2.0.5
2025-12-12 · diff ↗
2.0.4
2025-12-04 · diff ↗
2.0.3
2025-11-08 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.0.2
2025-03-25 · diff ↗
2.0.1
2025-02-13 · diff ↗

Show 13 earlier events

2.0.0
2024-07-07 · diff ↗
1.0.9
2024-05-30 · diff ↗
1.0.8
2024-05-16 · diff ↗
1.0.7
2024-05-10 · diff ↗
1.0.6
2024-04-29 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.5
2024-04-21 · diff ↗
1.0.4
2024-04-20 · diff ↗
1.0.3
2024-04-13 · diff ↗
1.0.2
2024-04-10 · diff ↗
1.0.1
2024-04-05 · diff ↗
1.0.0
2024-04-02
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-02
Total releases: 25 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 12 KB / 19 files
Download size: 2.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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