R Observatory: Metrics for DGCA version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2024-05-04. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 1.0.3, its last release before removal.

DGCA

1.0.3

Differential Gene Correlation Analysis

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Andrew McKenzie3 releasesCRAN page ↗

Performs differential correlation analysis on input matrices, with multiple conditions specified by a design matrix. Contains functions to filter, process, save, visualize, and interpret differential correlations of identifier-pairs across the entire identifier space, or with respect to a particular set of identifiers (e.g., one). Also contains several functions to perform differential correlation analysis on clusters (i.e., modules) or genes. Finally, it contains functions to generate empirical p-values for the hypothesis tests and adjust them for multiple comparisons. Although the package was built with gene expression data in mind, it is applicable to other types of genomics data as well, in addition to being potentially applicable to data from other fields entirely. It is described more fully in the manuscript introducing it, freely available at doi:10.1186/s12918-016-0349-1.

Install

R (source archive)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/DGCA/DGCA_1.0.3.tar.gz"
pkgFile <- "DGCA_1.0.3.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.0.3) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-dgca

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.15

not tracked

Coverage

100%

Documentation · exports

3

Dependencies · direct

Documentation

READMEYes · 221 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 18%

Downloads

DGCA Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on63 r2u

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.2

Imports (3)

WGCNA matrixStatsmethods

LinkingTo (0)

none

Suggests (19)

knitr impute gplots fdrtool testthat ggplot2 plotrix GOstats HGNChelper org.Hs.eg.db AnnotationDbi abind MEGENAMatrixdoMC igraph cowplotstatsutils

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Andrew McKenzie

Author, Maintainer

Authors (2)

Andrew McKenzie

Author, Maintainer

Bin Zhang

Author

Package Timeline

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

R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2024-05-04
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.3
2023-03-15 · diff ↗
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
1.0.2
2019-12-09 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.0.1
2016-11-17
R
R 3.3.0 released · 2016-05-03

Package metadata

Total releases: 3
License: GPL-3 OSI
Minimum R: ≥ 3.2
Bundled data: 436 KB / 3 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DGCA")

Format

Zhang, B., & McKenzie, A. (n.d.). DGCA: Differential Gene Correlation Analysis (Version 1.0.3) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=DGCA

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 DGCA version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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