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: 1.0.3
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 ORCID iD [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

Documentation:

Reference manual: GencoDymo2.html , GencoDymo2.pdf
Vignettes: GencoDymo2_vignette (source, R code)

Downloads:

Package source: GencoDymo2_1.0.3.tar.gz
Windows binaries: r-devel: GencoDymo2_1.0.3.zip, r-release: GencoDymo2_1.0.3.zip, r-oldrel: GencoDymo2_1.0.3.zip
macOS binaries: r-release (arm64): GencoDymo2_1.0.3.tgz, r-oldrel (arm64): not available, r-release (x86_64): GencoDymo2_1.0.3.tgz, r-oldrel (x86_64): not available
Old sources: GencoDymo2 archive

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