PMScanR

Protein motifs analysis and visualisation

Bioconductor version: 3.23 · Package version: 1.2.0

Other Bioconductor versions

devel is the development version; release is the current stable one.

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.

DOI: 10.18129/B9.bioc.PMScanR

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PMScanR")

Details

Maintainer	Jan Pawel Jastrzebski <bioinformatyka@gmail.com>
Author	Jan Pawel Jastrzebski [aut, cre] (ORCID: <https://orcid.org/0000-0001-8699-7742>), Monika Gawronska [ctb] (ORCID: <https://orcid.org/0009-0001-2677-6371>), Wiktor Babis [ctb] (ORCID: <https://orcid.org/0009-0006-3648-3413>), Miriana Quaranta [ctb] (ORCID: <https://orcid.org/0009-0003-0855-485X>), Damian Czopek [ctb, aut] (ORCID: <https://orcid.org/0009-0005-3471-4866>)
License	GPL-3
URL	https://github.com/prodakt/PMScanR
Bug Reports	https://github.com/prodakt/PMScanR/issues
System Requirements	Perl
Source branch	RELEASE_3_23
Build report	Bioconductor build system, r-universe
biocViews	MotifDiscovery, Software, Visualization
Package Short Url	https://bioconductor.org/packages/PMScanR/

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 1.2.0, https://bioconductor.org/packages/PMScanR.

Generated from the package metadata; it may differ from the package's own citation.

Documentation

PMScanR: An R Package for the large-scale identification, analysis, and visualization of protein motifs

Download

Follow the installation instructions to use this package in your R session.

Source package	PMScanR_1.2.0.tar.gz
Windows binary (x86_64)	PMScanR_1.2.0.zip
macOS binary (arm64)	PMScanR_1.2.0.tgz
macOS binary (x86_64)	PMScanR_1.2.0.tgz

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)