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.

Version:	1.0.4
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:	2026-01-12
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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