R Observatory: Metrics for modACDC version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

modACDC

2.0.1Package record

Association of Covariance for Detecting Differential Co-Expression

0packages depend

2.8Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Katelyn QueenCRAN 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. 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-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). 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

2NOTE11OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘tibble’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 2.0 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-06-09
ERROR10 OK, 2 NOTE, 1 ERROR2026-06-08
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

READMEYes · 239 wordsVignettesNoNEWSYes · 100% structured · does not mention 2.0.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 10
Examples that run: 80%8 run in a plain check · 2 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 100%

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #20,625 · ~8/day · ~233/mo

Releases R versions

Daily download trend is not available in this view yet.

26630 days

64790 days

2.8K1 year

Compare downloads with other packages →

Also on67 r2u4 autocran

How downloads are counted

Repository

uscbiostats/acdc ↗Organization: USCbiostats

1Stars

0Forks

0Open issues

0Open PRs

2Releases

98Commits

2Commit identities

98 commits · Last activity 2024-04-09

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2024-03-26 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/uscbiostats/acdc on 2026-10-21.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing modACDC adds 53 packages (29 with compiled code, 42 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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.

How these are counted

Code & Tests

People & History

People (2)

Katelyn Queen

Joshua Millstein

Author, Copyright holder

Releases (3)

Pick two releases to compare their code metrics.

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
record
2024-01-30 · current release · diff ↗
2.0.0
record
2024-01-25 · diff ↗ ·
added 3 exports
GCTA_par, GCTA_parPlot, GCTA_singleValue
1.0.0
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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