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GencoDymo2: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs
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.
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Package details |
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| Author | Monah Abou Alezz [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-2006-4250>), Lorenzo Salviati [ctb], Roberta Alfieri [ctb], Silvia Bione [ctb] |
| Maintainer | Monah Abou Alezz <aboualezz.monah@hsr.it> |
| License | GPL (>= 3) |
| Version | 1.0.1 |
| URL | https://github.com/monahton/GencoDymo2 https://monahton.github.io/GencoDymo2/ |
| Package repository | View on CRAN |
| Installation |
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