PMScanR
This is the development version of PMScanR; for the stable release version, see PMScanR.
Protein motifs analysis and visualisation
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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.
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 | ||
| NEWS | Text |
Details
| biocViews | MotifDiscovery, Software, Visualization |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | PMScanR_1.3.0.zip |
| macOS Binary (big-sur-x86_64) | PMScanR_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/PMScanR/ |
| Package Short Url | https://bioconductor.org/packages/PMScanR/ |
| Package Downloads Report | Download Stats |