PMScanR
This is the development version of PMScanR; to use it, please install the devel version of Bioconductor.
Protein motifs analysis and visualisation
Bioconductor version: Development (3.22)
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("PMScanR")):
Installation
To install this package, start R (version "4.5") 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.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PMScanR")| PMScanR: Protein Motif Scanning and Analysis | HTML | R Script |
| Reference Manual |
Details
| biocViews | MotifDiscovery, Software, Visualization |
| Version | 0.99.6 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| License | GPL-3 |
| Depends | |
| Imports | dplyr (>= 1.1.0), shiny, bslib, shinyFiles, plotly, rtracklayer, reshape2, ggseqlogo, ggplot2, seqinr, magrittr, rlang, utils, stringr, BiocFileCache |
| System Requirements | Perl |
| URL | https://github.com/prodakt/PMScanR |
| Bug Reports | https://github.com/prodakt/PMScanR/issues |
See More
| Suggests | BiocStyle, knitr, seqLogo, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PMScanR_0.99.6.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | PMScanR_0.99.6.tgz |
| macOS Binary (arm64) | PMScanR_0.99.6.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PMScanR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PMScanR |
| Bioc Package Browser | https://code.bioconductor.org/browse/PMScanR/ |
| Package Short Url | https://bioconductor.org/packages/PMScanR/ |
| Package Downloads Report | Download Stats |