R Observatory: Metrics for modACDC version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

modACDC

2.0.1

Association of Covariance for Detecting Differential Co-Expression

0packages depend

2.8Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Katelyn QueenFirst published 2023-05-103 releasesCRAN page ↗GitHub ↗

A series of functions to implement association of covariance for detecting differential co-expression (ACDC), a novel approach for detection of differential co-expression that simultaneously accommodates multiple phenotypes or exposures with binary, ordinal, or continuous data types. Users can use the default method which identifies modules by Partition or may supply their own modules. Also included are functions to choose an information loss criterion (ILC) for Partition using OmicS-data-based Complex trait Analysis (OSCA) and Genome-wide Complex trait Analysis (GCTA). The manuscript describing these methods is as follows: Queen K, Nguyen MN, Gilliland F, Chun S, Raby BA, Millstein J. "ACDC: a general approach for detecting phenotype or exposure associated co-expression" (2023) doi:10.3389/fmed.2023.1118824.

Install

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

install.packages("modACDC", 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("USCbiostats/ACDC")

Development version from USCbiostats/ACDC. 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-modacdc

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-modACDC

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-modACDC

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 2.2 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

13

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 239 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

2.8K

CRAN downloads in the past year

Rank #19,755 · ~8/day · ~236/mo

Releases R versions

Daily download trend is not available in this view yet.

11530 days

55590 days

2.8K1 year

Compare downloads with other packages →

Also on98 r2u15 autocran

Repository

GitHub ↗ uscbiostats/acdc

1Stars

0Forks

0Open issues

0Open PRs

2Releases

98Commits

2Contributors

98 commits · Last activity 2024-04-09

Stars over time

2024-03-26 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/uscbiostats/acdc on 2026-08-16.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (13)

CCP data.table doParallel foreach genieclust genio ggplot2 partitionparalleltibble tidyrtoolsutils

LinkingTo (0)

none

Suggests (1)

CCA

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Katelyn Queen

Author, Maintainer, Copyright holder

Authors (2)

Katelyn Queen

Author, Maintainer, Copyright holder

Joshua Millstein

Author, Copyright holder

Copyright holders (2)

Katelyn Queen

Author, Maintainer, Copyright holder

Joshua Millstein

Author, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.0.1Latest
2024-01-30 · current release · diff ↗
2.0.0
2024-01-25 · diff ↗
1.0.0
2023-05-10
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-05-10
Total releases: 3 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 20 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("modACDC")

Format

Queen, K., & Millstein, J. (2024). modACDC: Association of Covariance for Detecting Differential Co-Expression (Version 2.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.modACDC

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 modACDC version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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