{ "_id": "6a1abd7a1d7bb097a09d61cb", "Package": "PMScanR", "Title": "Protein motifs analysis and visualisation", "Version": "1.3.0", "Authors@R": "c(\nperson(given = \"Jan Pawel\",\nfamily = \"Jastrzebski\",\nrole = c(\"aut\", \"cre\"),\nemail = \"bioinformatyka@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8699-7742\")),\nperson(given = \"Monika\",\nfamily = \"Gawronska\",\nrole = c(\"ctb\"),\nemail = \"gawronska572@gmail.com\",\ncomment = c(ORCID = \"0009-0001-2677-6371\")),\nperson(given = \"Wiktor\",\nfamily = \"Babis\",\nrole = c(\"ctb\"),\nemail = \"wiktorbabis@gmail.com\",\ncomment = c(ORCID = \"0009-0006-3648-3413\")),\nperson(given = \"Miriana\",\nfamily = \"Quaranta\",\nrole = c(\"ctb\"),\nemail = \"miriana.quaranta@uniroma1.it\",\ncomment = c(ORCID = \"0009-0003-0855-485X\")),\nperson(given = \"Damian\",\nfamily = \"Czopek\",\nrole = c(\"ctb\", \"aut\"),\nemail = \"dcwmpl@gmail.com\",\ncomment = c(ORCID = \"0009-0005-3471-4866\")))", "Description": "Provides tools for large-scale protein motif analysis and\nvisualization in R. PMScanR facilitates the identification of\nmotifs using external tools like PROSITE's ps_scan (handling\nnecessary file downloads and execution) and enables downstream\nanalysis of results. Key features include parsing scan outputs,\nconverting formats (e.g., to GFF-like structures), generating\nmotif occurrence matrices, and creating informative\nvisualizations such as heatmaps, sequence logos (via\nseqLogo/ggseqlogo). The package also offers an optional\nShiny-based graphical user interface for interactive analysis,\naiming to streamline the process of exploring motif patterns\nacross 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", "SystemRequirements": "Perl", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibuv1-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": { "Date": "2026-05-30 07:11:02 UTC", "User": "root" }, "Author": "Jan Pawel Jastrzebski [aut, cre] 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