PMScanR
This is the development version of PMScanR; for the stable release version, see PMScanR.
All Bioconductor versions of PMScanR
3.24 (devel), 3.23 (release), 3.22
Protein motifs analysis and visualisation
Bioconductor version: 3.24 · Package version: 1.3.0
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.
Author: Jan Pawel Jastrzebski [aut, cre] 
, Monika Gawronska [ctb] , Wiktor Babis [ctb] , Miriana Quaranta [ctb] , Damian Czopek [ctb, aut]
Maintainer: Jan Pawel Jastrzebski <bioinformatyka at gmail.com>
Citation
From within R, enter citation("PMScanR"):
Jan Pawel Jastrzebski, Damian Czopek. PMScanR: Protein motifs analysis and visualisation. doi:10.18129/B9.bioc.PMScanR, R package version 1.3.0, https://bioconductor.org/packages/PMScanR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("PMScanR")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.3.0 |
| License | GPL-3 |
| URL | https://github.com/prodakt/PMScanR |
| Bug Reports | https://github.com/prodakt/PMScanR/issues |
| System Requirements | Perl |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.22 (R-4.5) (less than a year) |
| Downloads rank | 2216 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | MotifDiscovery, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/PMScanR/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PMScanR")| PMScanR: An R Package for the large-scale identification, analysis, and visualization of protein motifs | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | PMScanR_1.3.0.tar.gz |
| Windows binary (x86_64) | PMScanR_1.3.0.zip |
| macOS binary (arm64) | PMScanR_1.3.0.tgz |
| macOS binary (x86_64) | PMScanR_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PMScanR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PMScanR |
| Package Downloads Report | Download Stats |
Dependencies
Imports: dplyr (>= 1.1.0), shiny, bslib, shinyFiles, plotly, rtracklayer, reshape2, ggseqlogo, ggplot2, seqinr, magrittr, rlang, utils, stringr, BiocFileCache
Suggests: BiocStyle, knitr, seqLogo, rmarkdown, testthat (>= 3.0.0)