Package: PMScanR
Title: Protein motifs analysis and visualisation
Version: 1.3.0
Authors@R: c(
    person(given = "Jan Pawel",
           family = "Jastrzebski",
           role = c("aut", "cre"),
           email = "bioinformatyka@gmail.com",
           comment = c(ORCID = "0000-0001-8699-7742")),
	person(given = "Monika",
           family = "Gawronska",    
           role = c("ctb"),
		   email = "gawronska572@gmail.com",
           comment = c(ORCID = "0009-0001-2677-6371")), 
    person(given = "Wiktor",
           family = "Babis",        
           role = c("ctb"),          
           email = "wiktorbabis@gmail.com",
		   comment = c(ORCID = "0009-0006-3648-3413")),
	person(given = "Miriana",
           family = "Quaranta",        
           role = c("ctb"),          
           email = "miriana.quaranta@uniroma1.it",
		   comment = c(ORCID = "0009-0003-0855-485X")),
	person(given = "Damian",
           family = "Czopek",        
           role = c("ctb", "aut"),          
           email = "dcwmpl@gmail.com",
		   comment = c(ORCID = "0009-0005-3471-4866")))
Description: 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.
URL: https://github.com/prodakt/PMScanR
BugReports: https://github.com/prodakt/PMScanR/issues
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
biocViews: MotifDiscovery, Visualization
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)
SystemRequirements: Perl
Config/testthat/edition: 3
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libuv1-dev libxml2-dev libssl-dev perl xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:05:36 UTC
RemoteUrl: https://github.com/bioc/PMScanR
RemoteRef: HEAD
RemoteSha: c144ba8543630ae68ca7ed7b3a1dd116d7082559
NeedsCompilation: no
Packaged: 2026-07-07 06:06:08 UTC; root
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>)
Maintainer: Jan Pawel Jastrzebski <bioinformatyka@gmail.com>