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.
Version: 1.0.1 Imports: Biostrings (≥ 2.72.1), BSgenome (≥ 1.66.3), BSgenome.Hsapiens.UCSC.hg38 (≥ 1.4.5), 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), tools (≥ 4.4.0), utils (≥ 4.4.0) Suggests: devtools (≥ 2.4.5), IRanges (≥ 2.38.1), knitr, rmarkdown, testthat (≥ 3.0.0) Published: 2025-05-15 DOI: 10.32614/CRAN.package.GencoDymo2 Author: Monah Abou Alezz [aut, cre, cph], Lorenzo Salviati [ctb], Roberta Alfieri [ctb], Silvia Bione [ctb] Maintainer: Monah Abou Alezz <aboualezz.monah at hsr.it> BugReports: https://github.com/monahton/GencoDymo2/issues License: GPL (≥ 3) URL: https://github.com/monahton/GencoDymo2, https://monahton.github.io/GencoDymo2/ NeedsCompilation: no Language: en-US Citation: GencoDymo2 citation info Materials: README NEWS CRAN checks: GencoDymo2 results [issues need fixing before 2025-08-25] Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=GencoDymo2 to link to this page.
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