R Observatory: Metrics for TFactSR version 0.99.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TFactSR

0.99.0

Enrichment Approach to Predict Which Transcription Factors are Regulated

0packages depend

1.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Atsushi FukushimaFirst published 2023-08-311 releasesCRAN page ↗

R implementation of 'TFactS' to predict which are the transcription factors (TFs), regulated in a biological condition based on lists of differentially expressed genes (DEGs) obtained from transcriptome experiments. This package is based on the 'TFactS' concept by Essaghir et al. (2010) doi:10.1093/nar/gkq149 and expands it. It allows users to perform 'TFactS'-like enrichment approach. The package can import and use the original catalogue file from the 'TFactS' as well as users' defined catalogues of interest that are not supported by 'TFactS' (e.g., Arabidopsis).

Install

R (CRAN)Ubuntu (r2u)

install.packages("TFactSR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-tfactsr

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

Health

CRAN checks

13OK

Slowest check: 1.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.17

not tracked

Coverage

100%

Documentation · exports

2

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 11 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 78%

Downloads

1.7K

CRAN downloads in the past year

Rank #22,082 · ~5/day · ~145/mo

Releases R versions

Daily download trend is not available in this view yet.

14430 days

50990 days

1.7K1 year

Compare downloads with other packages →

Also on100 r2u

Repository

GitHub ↗ afukushima/tfactsr

0Stars

1Forks

1Open issues

0Open PRs

0Releases

30Commits

2Contributors

30 commits · Last activity 2023-09-01

Forks over time

2023-08-19 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/afukushima/tfactsr on 2026-08-23.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.3.0

Imports (2)

qvaluestats

LinkingTo (0)

none

Suggests (5)

BiocStyle knitr rmarkdown spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Atsushi Fukushima

Author, Maintainer

Authors (1)

Atsushi Fukushima

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.99.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2023-08-31
Total releases: 1 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.3.0
Bundled data: 116 KB / 7 files
Download size: 418 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TFactSR")

Format

Fukushima, A. (2023). TFactSR: Enrichment Approach to Predict Which Transcription Factors are Regulated (Version 0.99.0) [Computer software]. https://doi.org/10.32614/CRAN.package.TFactSR

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 TFactSR version 0.99.0 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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