GencoDymo2: Comprehensive Analysis of 'GENCODE' Annotations and Splice SiteMotifs
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: | 1.0.3 |
| 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) |
| Published: | 2025-08-21 |
| 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 |
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