R Observatory: Metrics for scregclust version 0.2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scregclust

0.2.4

Reconstructing the Regulatory Programs of Target Genes in scRNA-Seq Data

0packages depend

3.2Kdownloads / year

35.4%test coverage

13/13checks pass

Overview

About

Maintained by Felix HeldFirst published 2024-11-216 releasesCRAN page ↗GitHub ↗

Implementation of the scregclust algorithm described in Larsson, Held, et al. (2024) doi:10.1038/s41467-024-53954-3 which reconstructs regulatory programs of target genes in scRNA-seq data. Target genes are clustered into modules and each module is associated with a linear model describing the regulatory program.

Install

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

install.packages("scregclust", 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("scmethods/scregclust")

Development version from scmethods/scregclust. 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-scregclust

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-scregclust

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-scregclust

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

Health

CRAN checks

13OK

Slowest check: 4.4 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.01

35.4%

Coverage · measured lines

100%

Documentation · exports

13

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 144 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: not tracked
Documented parameters: 99%
Return-value docs: 100%
References docs: 19%

Downloads

3.2K

CRAN downloads in the past year

Rank #8,835 · ~9/day · ~267/mo

Releases R versions

Daily download trend is not available in this view yet.

22630 days

1K90 days

3.2K1 year

Compare downloads with other packages →

Also on402 r2u28 autocran

Repository

GitHub ↗ scmethods/scregclust

14Stars

3Forks

1Open issues

0Open PRs

5Releases

142Commits

3Contributors

clusteringscrna-seq-analysisregulatory-programs

License GPL-3.0 · 142 commits · Last activity 2026-05-03 · 0% stars, 30d

Stars over time

2025-07-08 · 132026-07-07 · 14

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/scmethods/scregclust on 2026-08-23.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (13)

Matrixstatsmethodsutilsreshape igraphgraphicsgridcli prettyunits ggplot2 rlang Rcpp

LinkingTo (2)

Rcpp RcppEigen

Suggests (6)

testthat quarto Seurat hdf5r glmGamPoi GEOquery

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Felix Held

Author, Maintainer

Authors (3)

Felix Held

Author, Maintainer

Ida Larsson

Author

Sven Nelander

Author

Contributors (1)

André Armatowski

Contributor · added in 0.2.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.2.4Latest
2026-04-06 · current release · diff ↗
0.2.3
2026-04-05 · diff ↗
0.2.2
2025-07-27 · diff ↗
0.2.1
2025-07-24 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.2.0
2024-12-06 · diff ↗
0.1.10
2024-11-21
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-11-21
Total releases: 6 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Download size: 286 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scregclust")

Format

Held, F., Armatowski, A., Larsson, I., & Nelander, S. (2026). scregclust: Reconstructing the Regulatory Programs of Target Genes in scRNA-Seq Data (Version 0.2.4) [Computer software]. https://doi.org/10.32614/CRAN.package.scregclust

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 scregclust version 0.2.4 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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