Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs R package GencoDymo2 version 1.0.4 A comprehensive suite of helper functions designed to facilitate the analysis of genomic annotations from the 'GENCODE' database <https://www.gencodegenes.org/>, supporting both human and mouse genomes. This toolkit enables users to extract, filter, and analyze a wide range of annotation features including genes, transcripts, exons, and introns across different 'GENCODE' releases. It provides functionality for cross-version comparisons, allowing researchers to systematically track annotation updates, structural changes, and feature-level differences between releases. In addition, the package can generate high-quality FASTA files containing donor and acceptor splice site motifs, which are formatted for direct input into the 'MaxEntScan' tool (Yeo and Burge, 2004 <doi:10.1089/1066527041410418>), enabling accurate calculation of splice site strength scores. Software Imports: Biostrings (>= 2.72.1), BSgenome (>= 1.66.3), data.table (>= 1.17.0), dplyr (>= 1.1.4), GenomicRanges (>= 1.56.2), methods (>= 4.4.0), plotrix (>= 3.8.4), progress (>= 1.2.3), RCurl (>= 1.98.1.17), rtracklayer (>= 1.64.0), tidyr (>= 1.3.1), IRanges (>= 2.38.1), tools (>= 4.4.0), utils (>= 4.4.0) Suggests: devtools (>= 2.4.5), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.5), knitr, rmarkdown, testthat (>= 3.0.0) Monah Abou Alezz <aboualezz.monah@hsr.it> Comprehensive R Archive Network (CRAN) Monah Abou Alezz [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-2006-4250>), Lorenzo Salviati [ctb], Roberta Alfieri [ctb], Silvia Bione [ctb] GPL (>= 3) 2026-01-12 application/tgz https://CRAN.R-project.org/package=GencoDymo2 doi:10.32614/CRAN.package.GencoDymo2 en-US