R Observatory: Metrics for scregclust version 0.2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scregclust

0.2.4Package record

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

0packages depend

3.6Kdownloads / year

35.5%test coverage

13/13flavors OK

Overview

About

Maintained by Felix HeldCRAN page ↗GitHub ↗Website ↗Issues ↗

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. 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-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). 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: 4.2 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.4

READMEYes · 144 wordsVignettesNoNEWSYes · 100% structured · does not mention 0.2.4Citation fileYes · cites a publicationWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 31 (16 internal)includes a package overview page
Examples that run: no examples
Exported functions with examples: 0%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 19%

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #9,906 · ~10/day · ~304/mo

Releases R versions

Daily download trend is not available in this view yet.

35030 days

1K90 days

3.6K1 year

Compare downloads with other packages →

Also on358 r2u4 autocran

How downloads are counted

Repository

scmethods/scregclust ↗Organization: scmethods

15Stars

3Forks

1Open issues

0Open PRs

5Releases

142Commits

3Commit identities

clusteringscrna-seq-analysisregulatory-programs

License file reads as GPL-3.0 · 142 commits · Last activity 2026-05-03 · 0% stars, 30d · Default branch at 0.2.5, ahead of CRAN 0.2.4 (checked 2026-10-25)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 7
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-07-08 · 132026-09-09 · 15

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/scmethods/scregclust on 2026-10-25.

Continuous integration (1)

GitHub Actions

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-05-03 · The repository has a site deploy workflow

pkgdown site last built 2026-05-03

CRAN release process (1)

cran-comments.md

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing scregclust adds 25 packages (12 with compiled code, 23 MB of source tarballs). Heaviest: ggplot2 6.0 MB, igraph 4.8 MB, Rcpp 1.8 MB.

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.

How these are counted

Code & Tests

People & History

People (4)

Felix Held

Author, Maintainer since 0.1.10 (2024)

Ida Larsson

Author

Sven Nelander

Author

André Armatowski

Contributor · added in 0.2.0

Releases (6)

Pick two releases to compare their code metrics.

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

Cite

Cite this package

Run in R for the authors' entry:

citation("scregclust")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1038/s41467-024-53954-3.

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 v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →