RQdeltaCT

1.3.3

Relative Quantification of Gene Expression using Delta Ct Methods

0packages depend

8Kdownloads / year

0.0%test coverage

13/13checks pass

Overview

About

Maintained by Daniel ZalewskiFirst published 2024-04-024 releasesCRAN page ↗

The commonly used methods for relative quantification of gene expression levels obtained in real-time PCR (Polymerase Chain Reaction) experiments are the delta Ct methods, encompassing 2^-dCt and 2^-ddCt methods, originally proposed by Kenneth J. Livak and Thomas D. Schmittgen (2001) doi:10.1006/meth.2001.1262. The main idea is to normalise gene expression values using endogenous control gene, present gene expression levels in linear form by using the 2^-(value)^ transformation, and calculate differences in gene expression levels between groups of samples (or technical replicates of a single sample). The 'RQdeltaCT' package offers functions that cover both methods for comparison of either independent groups of samples or groups with paired samples, together with importing expression datasets, performing multi-step quality control of data, enabling numerous data visualisations, enrichment of the standard workflow with additional useful analyses (correlation analysis, Receiver Operating Characteristic analysis, logistic regression), and conveniently export obtained results in table and image formats. The package has been designed to be friendly to non-experts in R programming.

Install

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

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

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

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-rqdeltact

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-RQdeltaCT

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-RQdeltaCT

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

Health

CRAN checks

13OK

Slowest check: 7.9 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

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 289 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 94%
Return-value docs: 100%
References docs: 0%

Downloads

CRAN downloads in the past year

Rank #4,970 · ~22/day · ~665/mo

Releases R versions

Daily download trend is not available in this view yet.

43630 days

1.9K90 days

8K1 year

Compare downloads with other packages →

Also on150 r2u16 autocran

Repository

GitHub ↗ donadelnal/rqdeltact

1Stars

0Forks

2Open issues

0Open PRs

0Releases

72Commits

3Contributors

72 commits · Last activity 2025-09-14 · 0% stars, 30d

Stars over time

2025-07-26 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/donadelnal/rqdeltact on 2026-07-19.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (20)

tidyverse dplyr ggplot2 magrittr tidyr tidyselect coin ctrlGene ggsignif Hmisc corrplot ggpmisc pROC oddsratiostatsgraphicsgrDevicesutilspheatmap GGally

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 5,546 (40%)Rd 3,065 (22%)Vignettes 2,977 (22%)Other 2,179 (16%)

Code characteristics

Cyclomatic complexity: 5.0 median / 18 max
Test cases: 1 / 0.00 per code line

Test coverage

Line coverage

Expression

0.0%

Tests / Examples

0.0% / 61% ex

Functions

32 32 exported

Complexity

6.2 avg / 18 max

Call network

32 nodes / 1 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

32 functions

Function	Cyclo	Coverage
FCh_plot exp	18	0%
ROCh exp	7	0%
RQ_dCt exp	10	0%
RQ_ddCt exp	10	0%
control_Ct_barplot_gene exp	4	0%
control_Ct_barplot_sample exp	4	0%

Datasets

Bundled datasets · 4

Name	Class	Rows × Cols	Also ships in
data.Ct	data.frame	1,288 × 5	–
data.Ct.10vs10	data.frame	410 × 5	–
data.Ct.3groups	data.frame	2,048 × 5	–
data.Ct.pairwise	tbl_df/tbl/data.frame	756 × 4	–

People & History

People (1)

Maintainer (1)

Daniel Zalewski

Author, Maintainer

Authors (1)

Daniel Zalewski

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.3.3Latest
2025-09-14 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.3.2
2025-02-13 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.3.0
2024-04-17 · diff ↗
1.2.1
2024-04-02
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-02
Total releases: 4 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 13 KB / 4 files
Download size: 3.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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