R Observatory: Metrics for deltaccd version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

deltaccd

1.0.2Package record

Quantify Rhythmic Gene Co-Expression Relative to a Reference

0packages depend

3.4Kdownloads / year

95.5%test coverage

13/13flavors OK

Overview

About

Maintained by Jake HugheyCRAN page ↗GitHub ↗Website ↗

Infer progression of circadian rhythms in transcriptome data in which samples are not labeled with time of day and coverage of the circadian cycle may be incomplete. See Shilts et al. (2018) doi:10.7717/peerj.4327.

Changes in 1.0.2

Updated examples.

From NEWS.md in the release

Install

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

install.packages("deltaccd", 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("hugheylab/deltaccd")

Development version from hugheylab/deltaccd. 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-deltaccd

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-deltaccd

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-deltaccd

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: 1.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.2

README· In the repository, left out of the releaseVignettesNoNEWSYes · 100% structured · mentions 1.0.2Citation fileNoWebsiteYes · pkgdown

Help pages: 6
Examples that run: 100%4 run in a plain check
Exported functions with examples: 80%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #15,022 · ~9/day · ~280/mo

Releases R versions

Daily download trend is not available in this view yet.

27830 days

81190 days

3.4K1 year

Compare downloads with other packages →

Also on71 r2u12 autocran

How downloads are counted

Repository

hugheylab/deltaccd ↗Organization: hugheylab

1Stars

0Forks

0Open issues

0Open PRs

1Releases

143Commits

4Commit identities

143 commits · Last activity 2022-12-01 · 0% stars, 30d · Default branch at 1.0.4, ahead of CRAN 1.0.2 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2026-05-12 · 12026-07-07 · 1

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/hugheylab/deltaccd on 2026-10-22.

Continuous integration (1)

GitHub Actions

Docs source (2)

pkgdown

GitHub Pages site last deployed 2020-05-08

pkgdown site last built 2022-12-01

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 1 practice

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing deltaccd adds 24 packages (10 with compiled code, 20 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, isoband 1.5 MB.

Depends (1)

R >= 3.4

Imports (7)

doRNG foreach ggplot2 rlang scales statmod data.table

LinkingTo (0)

none

Suggests (5)

doParallel knitr rmarkdown testthat (>= 3.0.0)vdiffr

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 (2)

Jake Hughey

Author, Maintainer since 1.0.2 (2022)

Elliot Outland

Author

Releases (1)

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.0.2Latest
record
2022-02-11 · current release
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-02-11
Total releases: 1 / 4 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.4
Bundled data: 782 KB / 1 file
Download size: 813 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("deltaccd")

Format

Hughey, J., & Outland, E. (2022). deltaccd: Quantify Rhythmic Gene Co-Expression Relative to a Reference (Version 1.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.deltaccd

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 deltaccd version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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