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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.

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 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.pdf
Vignettes: GencoDymo2_vignette (source, R code)

Downloads:

Package source: GencoDymo2_1.0.1.tar.gz
Windows binaries: r-devel: not available, r-release: GencoDymo2_1.0.1.zip, r-oldrel: not available
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

Please use the canonical form https://CRAN.R-project.org/package=GencoDymo2 to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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