PMScanR

This is the development version of PMScanR; for the stable release version, see PMScanR.

Protein motifs analysis and visualisation

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DOI: 10.18129/B9.bioc.PMScanR

Bioconductor version: Development (3.23)

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] ORCID iD ORCID: 0000-0001-8699-7742 , Monika Gawronska [ctb] ORCID iD ORCID: 0009-0001-2677-6371 , Wiktor Babis [ctb] ORCID iD ORCID: 0009-0006-3648-3413 , Miriana Quaranta [ctb] ORCID iD ORCID: 0009-0003-0855-485X , Damian Czopek [ctb, aut] ORCID iD ORCID: 0009-0005-3471-4866

Maintainer: Jan Pawel Jastrzebski <bioinformatyka at gmail.com>

Citation (from within R, enter citation("PMScanR")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("PMScanR")

For older versions of R, please refer to the appropriate Bioconductor release.