R Observatory: Metrics for TFactSR version 0.99.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TFactSR

0.99.0Package record

Enrichment Approach to Predict Which Transcription Factors are Regulated

0packages depend

2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Atsushi FukushimaCRAN page ↗Website ↗

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).

Changes in 0.99.0

Package released

From inst/NEWS in the release

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. 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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.6 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 0.99.0

READMEYes · 11 wordsVignettesYes · 1 · dynamicNEWSYes · 0% structured · mentions 0.99.0Citation fileNoWebsiteYes · pkgdown

Help pages: 18includes a package overview page
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 78%

Vignettes (1)

TFactSR

How these are measured

Downloads

2K

CRAN downloads in the past year

Rank #20,801 · ~5/day · ~164/mo

Releases R versions

Daily download trend is not available in this view yet.

24930 days

63490 days

2K1 year

Compare downloads with other packages →

Also on72 r2u

How downloads are counted

Repository

afukushima/tfactsr ↗Account: afukushima

0Stars

1Forks

1Open issues

0Open PRs

0Releases

30Commits

2Commit identities

30 commits · Last activity 2023-09-01 · Default branch at 0.99.1, ahead of CRAN 0.99.0 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 0

Forks over time

2023-08-19 · 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/afukushima/tfactsr on 2026-10-18.

Continuous integration (1)

GitHub Actions

Docs source (1)

GitHub Pages site last deployed 2023-08-19

Coverage (1)

Coverage reporting

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing TFactSR adds 0 packages. 1 more not on CRAN is not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Atsushi Fukushima

Author, Maintainer since 0.99.0 (2023)

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
0.99.0Latest
record
2023-08-31 · current release
R
R 4.3.0 released · 2023-04-21

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

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 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 TFactSR version 0.99.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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