R Observatory: Metrics for RQdeltaCT version 1.3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RQdeltaCT

1.3.3Package record

Relative Quantification of Gene Expression using Delta Ct Methods

0packages depend

7.3Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Daniel ZalewskiCRAN page ↗GitHub ↗

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. 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-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). 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

13OK

CRAN check page ↗

Slowest check: 6.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-09
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.3

READMEYes · 289 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 36
Examples that run: 100%32 run in a plain check
Exported functions with examples: 100%
Documented parameters: 94%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

RQdeltaCT - Relative Quantification of Gene Expression using Delta Ct Methods HTML

How these are measured

Downloads

7.3K

CRAN downloads in the past year

Rank #7,658 · ~20/day · ~607/mo

Releases R versions

Daily download trend is not available in this view yet.

42230 days

1.2K90 days

7.3K1 year

Compare downloads with other packages →

Also on91 r2u4 autocran

How downloads are counted

Repository

donadelnal/rqdeltact ↗Account: Donadelnal

1Stars

0Forks

2Open issues

0Open PRs

0Releases

72Commits

3Commit identities

72 commits · Last activity 2025-09-14

Responsiveness

not measured

Stars over time

2025-07-26 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/donadelnal/rqdeltact on 2026-10-18.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing RQdeltaCT adds 141 packages (67 with compiled code, 110 MB of source tarballs). Heaviest: stringi 11 MB, TH.data 8.2 MB, ggplot2 6.0 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Daniel Zalewski

Author, Maintainer since 1.2.1 (2024)

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.3.3Latest
record
2025-09-14 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.3.2
record
2025-02-13 · diff ↗ ·
added 1 export
control_heatmap
R
R 4.4.0 released · 2024-04-24
1.3.0
record
2024-04-17 · diff ↗ ·
removed 4 exports
RQ_exp_Ct_dCt, RQ_plot, RQ_volcano, exp_Ct_dCt

added 3 exports
FCh_plot, RQ_dCt, results_volcano
1.2.1
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("RQdeltaCT")

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

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 RQdeltaCT version 1.3.3 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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