# PMScanR <img src="inst/img/PMlogo_3D.png" align="right" height = 150/>
`PMScanR` is an R package for the large-scale identification, analysis, and visualization of protein motifs. It integrates PROSITE's `ps_scan` tool, handles data conversion, and offers multiple visualization methods, including heatmaps and sequence logos. The package also features a full graphical user interface (GUI) via Shiny for a code-free experience.
## Installation
Once the package is accepted to Bioconductor, you will install it by starting R (version "4.4" or higher) and entering:
```r
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PMScanR")
```
## Quick Start
You can either launch the interactive application or run an analysis via the command line.
#### Interactive GUI
For a user-friendly, clickable interface that covers the entire analysis workflow, simply run:
```r
library(PMScanR)
runPMScanRShiny()
```
#### Command Line Example
```r
library(PMScanR)
# 1. Get path to the example FASTA file included with the package
fasta_file <- system.file("extdata", "hemoglobins.fasta", package = "PMScanR")
# 2. Run the motif scan and save results in GFF format
runPsScan(in_file = fasta_file, out_format = 'gff', out_file = "results_scan.gff")
# For a full, step-by-step guide, please see the package vignette:
browseVignettes("PMScanR")
```
