PMScanR
Bioc currentProtein motifs analysis and visualisation
Release Lineage
Entered 3.22 · Oct 30, 2025
Current · Requires R 4.6
Description
Provides tools for large-scale protein motif analysis and visualization in R. PMScanR facilitates the identification of motifs using external tools like PROSITE's ps_scan (handling necessary file downloads and execution) and enables downstream analysis of results. Key features include parsing scan outputs, converting formats (e.g., to GFF-like structures), generating motif occurrence matrices, and creating informative visualizations such as heatmaps, sequence logos (via seqLogo/ggseqlogo). The package also offers an optional Shiny-based graphical user interface for interactive analysis, aiming to streamline the process of exploring motif patterns across multiple protein sequences.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
19 10 exported
Complexity
5.5 avg / 32 max
Call network
19 nodes / 15 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
2,494
Files
45
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
10
Internal functions
7
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.10
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
6.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
1 externalPerl
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2025-11-28
Latest release
2026-04-28
Avg cadence
151 days
Cold removal rate
100%
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 11 (1 internal)includes a package overview page
- Examples that run
- 100%10 run in a plain check (2 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/prodakt/pmscanr on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| PROSITEoutput | – | – | – |
| out_Hb_gff | data.frame | 153 × 9 | No other package |
| out_Hb_psa | – | – | – |
Topics
People
- Jan Pawel Jastrzebski author maintainer
- Wiktor Babis contributor
- Damian Czopek contributor author
- Monika Gawronska contributor
- Miriana Quaranta contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("PMScanR")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.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.