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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "GencoDymo2" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'GencoDymo2: Comprehensive Analysis of ''GENCODE'' Annotations and Splice Site
  Motifs'
version: 1.0.4
doi: 10.3389/fgene.2020.00488
identifiers:
- type: doi
  value: 10.32614/CRAN.package.GencoDymo2
abstract: 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 <https://doi.org/10.1089/1066527041410418>), enabling
  accurate calculation of splice site strength scores.
authors:
- family-names: Abou Alezz
  given-names: Monah
  email: aboualezz.monah@hsr.it
  orcid: https://orcid.org/0000-0002-2006-4250
preferred-citation:
  type: article
  title: GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest
    Their Role in Gene Expression Regulation
  authors:
  - family-names: Abou Alezz
    given-names: Monah
    email: aboualezz.monah@hsr.it
    orcid: https://orcid.org/0000-0002-2006-4250
  - family-names: Celli
    given-names: Ludovica
  - family-names: Belotti
    given-names: Giulia
  - family-names: Lisa
    given-names: Antonella
  - family-names: Bione
    given-names: Silvia
  journal: Frontiers in Genetics
  year: '2020'
  volume: '11'
  doi: 10.3389/fgene.2020.00488
  start: '488'
repository: https://monahton.r-universe.dev
repository-code: https://github.com/monahton/GencoDymo2
commit: 98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27
url: https://monahton.github.io/GencoDymo2/
date-released: '2026-02-05'
contact:
- family-names: Abou Alezz
  given-names: Monah
  email: aboualezz.monah@hsr.it
  orcid: https://orcid.org/0000-0002-2006-4250
references:
- type: manual
  title: 'GencoDymo2: Comprehensive Analysis of GENCODE Annotations and Splice Site
    Motifs'
  authors:
  - family-names: Abou Alezz
    given-names: Monah
  year: '2025'
  notes: R package version 1.0.4
  url: https://github.com/monahton/GencoDymo2
  doi: 10.5281/zenodo.15302316