R Observatory: Metrics for scTenifoldNet version 1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scTenifoldNet

1.4

Construct and Compare scGRN from Single-Cell Transcriptomic Data

1packages depend

19.3Kdownloads / year

35.2%test coverage

13/13checks pass

Overview

About

Maintained by Daniel OsorioFirst published 2019-12-159 releasesCRAN page ↗GitHub ↗

A workflow based on machine learning methods to construct and compare single-cell gene regulatory networks (scGRN) using single-cell RNA-seq (scRNA-seq) data collected from different conditions. Uses principal component regression, tensor decomposition, and manifold alignment, to accurately identify even subtly shifted gene expression programs. See doi:10.1016/j.patter.2020.100139 for more details.

Install

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

install.packages("scTenifoldNet", 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("cailab-tamu/scTenifoldNet")

Development version from cailab-tamu/scTenifoldNet. 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-sctenifoldnet

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-scTenifoldNet

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-scTenifoldNet

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

Health

CRAN checks

13OK

Slowest check: 3.9 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.16

35.2%

Coverage · measured lines

100%

Documentation · exports

11

Dependencies · direct

Check history

OK2026-08-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 756 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 88%
Documented parameters: 100%
Return-value docs: 100%
References docs: 70%

Downloads

19.3K

CRAN downloads in the past year

Rank #2,480 · ~53/day · ~1.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

3.1K30 days

7.9K90 days

19.3K1 year

Compare downloads with other packages →

Also on123 r2u8 autocran24 c2d4u

Repository

GitHub ↗ cailab-tamu/sctenifoldnet

41Stars

5Forks

6Open issues

0Open PRs

4Releases

532Commits

7Contributors

manifold-alignmentdifferential-regulation-analysissingle-cellgene-regulatory-networkstensor-decomposition

532 commits · Last activity 2026-07-10 · +5.1% stars, 30d

Stars over time

2025-04-16 · 232026-08-13 · 41

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/cailab-tamu/sctenifoldnet on 2026-08-09.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (11)

Rcpp RSpectraMatrixmethodsstatsutilsMASScli furrr future RhpcBLASctl

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

scTenifoldKnk

Code & Tests

People & History

People (5)

Maintainer (1)

Daniel Osorio

Author, Maintainer

Authors (5)

Daniel Osorio

Author, Maintainer

James Cai

Author, Contributor, Thesis advisor

Jianhua Huang

Author, Contributor

Guanxun Li

Author, Contributor

Yan Zhong

Author, Contributor

Contributors (4)

James Cai

Author, Contributor, Thesis advisor

Jianhua Huang

Author, Contributor

Guanxun Li

Author, Contributor

Yan Zhong

Author, Contributor

Package Timeline

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

1.4Latest
2026-08-05 · current release · diff ↗
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
1.3
2021-10-29 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2.4
2020-11-17 · diff ↗
1.2.3
2020-08-26 · diff ↗
1.2.2
2020-05-13 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.2.1
2020-04-09 · diff ↗
1.2.0
2020-03-10 · diff ↗
1.1.0
2020-01-08 · diff ↗
1.0.0
2019-12-15

Show 1 earlier events

R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-12-15
Total releases: 9 / 7 yrs
License: GPL (>= 2) OSI
Download size: 33 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scTenifoldNet")

Format

Osorio, D., Cai, J., Huang, J., Li, G., & Zhong, Y. (2026). scTenifoldNet: Construct and Compare scGRN from Single-Cell Transcriptomic Data (Version 1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.scTenifoldNet

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 scTenifoldNet version 1.4 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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