Skip to content

seqLogo

Bioc current

Sequence logos for DNA sequence alignments

v1.78.0 · software · LGPL (>= 2)
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.0 · Apr 26, 2007

Current · Requires R 4.6

1.0 In 39 of 49 releases 3.23

Description

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

12 2 exported

Complexity

4.4 avg / 16 max

Call network

12 nodes / 15 edges

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

Call graph

Open call graph →
Loading call graph…

Lowest coverage

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

Code

Structure

Lines of code

2,280

Files

26

Compiled share

0%

Has compiled src

No

Language breakdown

R 676 (29.6%)Tests 1,202 (52.7%)Docs 160 (7%)Vignettes 242 (10.6%)

API

Exported functions

2

Internal functions

10

Testing & CI

Has tests

Yes

Test-to-code ratio

1.78

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.2

System requirements

–

C++ standard

–

License

LGPL (>= 2)

License flags

SPDX valid, OSI approved

History

Versions

39

First release

2007-04-24

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

2

LOC over versions

v2.0: 446 LOCv2.1: 456 LOCv2.2: 456 LOCv2.3: 456 LOCv2.4: 457 LOCv2.5: 459 LOCv2.6: 459 LOCv2.7: 459 LOCv2.8: 459 LOCv2.9: 459 LOCv2.10: 459 LOCv2.11: 459 LOCv2.12: 459 LOCv2.13: 459 LOCv2.14: 678 LOCv3.0: 678 LOCv3.1: 656 LOCv3.2: 656 LOCv3.3: 656 LOCv3.4: 656 LOCv3.5: 656 LOCv3.6: 656 LOCv3.7: 656 LOCv3.8: 656 LOCv3.9: 656 LOCv3.10: 656 LOCv3.11: 656 LOCv3.12: 2,281 LOCv3.13: 2,281 LOCv3.14: 2,281 LOCv3.15: 2,280 LOCv3.16: 2,280 LOCv3.17: 2,280 LOCv3.18: 2,280 LOCv3.19: 2,280 LOCv3.20: 2,280 LOCv3.21: 2,280 LOCv3.22: 2,280 LOCv3.23: 2,280 LOC

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

Documentation

Documentation
READMEYes · 183 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
82%
Return-value docs
100%
References docs
0%

Topics

Software › BiologicalQuestion › SequenceMatching

Depended on by (22)

Bioconductor (21)

BCRANK DiffLogo igvR IntEREst MAGAR motifcounter MotifDb PMScanR PWMEnrich RCAS riboSeqR scanMiR SPLINTER TENET TFBSTools universalmotif generegulation Logolas motifRG rGADEM spliceSites

CRAN (1)

kmeRtone

People

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("seqLogo")
Ivanek, R., & Bembom, O. (2026). seqLogo: Sequence logos for DNA sequence alignments (Version 1.78.0) [Computer software]. https://bioconductor.org/packages/seqLogo

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.

APA

Balamuta, J. J. (2026). R Observatory: Metrics for seqLogo version 1.78.0 [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.

Report a problem with this page →

Privacy choices

These apply to this browser and are stored on this device only. Nothing about your choice is sent to us.

Read the privacy policy