R Observatory: Metrics for TFBSTools version 1.50.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TFBSTools

Bioc current

Software Package for Transcription Factor Binding Site (TFBS) Analysis

v1.50.0 · software · GPL-2

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.13 · Oct 15, 2013

Current · Requires R 4.6

1.0 In 26 of 49 releases 3.23

Description

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

78 20 exported

Complexity

3.5 avg / 17 max

Call network

78 nodes / 36 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

9,250

Files

99

Compiled share

4.5%

Has compiled src

Yes

Language breakdown

R 5,070 (54.8%)C/C++/src 418 (4.5%)Tests 115 (1.2%)Docs 2,909 (31.4%)Vignettes 738 (8%)

API

Exported functions

57

Internal functions

52

Recent export changes

v3.5+1 parseMEMEOutput

Testing & CI

Has tests

Yes

Test-to-code ratio

0.02

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

78.3%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.2.2

System requirements

–

C++ standard

–

License

GPL-2

License flags

SPDX valid, OSI approved

History

Versions

26

First release

2013-10-14

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

22

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 62 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 78%
Documented parameters: 87%
Return-value docs: 97%
References docs: 27%

Topics

Software › BiologicalQuestion › MotifAnnotation

Software › BiologicalQuestion › GeneRegulation

Software › BiologicalQuestion › MotifDiscovery

Software › AssayDomain › Transcription

Software › WorkflowStep › Alignment

Depended on by (26)

CRAN (1)

Signac

People

Ge Tan author maintainer

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TFBSTools")

Format

Tan, G. (2026). TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis (Version 1.50.0) [Computer software]. https://bioconductor.org/packages/TFBSTools

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 TFBSTools version 1.50.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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