https://prodakt.r-universe.devRecent package updates in prodaktR-universehttps://github.com/prodakt.pnghttps://prodakt.r-universe.devTue, 28 Apr 2026 13:07:14 GMTbioinformatyka@gmail.com (Jan Pawel Jastrzebski)Provides a complete workflow for the identification, analysis, and functional annotation of long non-coding RNAs (lncRNAs) from RNA-Seq data. The package includes functions for filtering transcripts from GTF files, evaluating the performance of multiple coding potential prediction tools (e.g., CPC2, PLEK, CPAT), and summarizing their agreement. It enables systematic performance analysis of individual tools, "at least N" tool consensus, and all possible tool combinations. Functional analysis is supported through the identification of potential cis- and trans-acting interactions with protein-coding genes, followed by enrichment analysis. Results can be visualized using a variety of plots, including radar plots, clock plots, and interactive Sankey diagrams.https://github.com/r-universe/bioc/actions/runs/28731343841Tue, 28 Apr 2026 13:07:14 GMTlncRna1.1.0successhttps://bioc.r-universe.devhttps://github.com/bioc/lncRnalncRna.RmdlncRna.htmllncRna: A Comprehensive Pipeline for lncRNA Identification and Functional Analysis2025-12-17 11:46:562026-03-11 19:49:43bioinformatyka@gmail.com (Jan Pawel Jastrzebski)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.https://github.com/r-universe/bioc/actions/runs/28845139566Tue, 28 Apr 2026 13:05:36 GMTPMScanR1.3.0successhttps://bioc.r-universe.devhttps://github.com/bioc/PMScanRPMScanR.RmdPMScanR.htmlPMScanR: An R Package for the large-scale identification, analysis, and visualization of protein motifs2025-04-11 13:49:352025-09-26 07:34:16