Package: GencoDymo2
Type: Package
Title: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site
        Motifs
Version: 1.0.4
Authors@R: c(
    person("Monah", "Abou Alezz", email = "aboualezz.monah@hsr.it", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-2006-4250")),
    person("Lorenzo", "Salviati", email = "lorenzo.salviati01@universitadipavia.it", role = "ctb"),
    person("Roberta", "Alfieri", email = "roberta.alfieri@igm.cnr.it", role = "ctb"),
    person("Silvia", "Bione", email = "bione@igm.cnr.it", role = "ctb"))
Maintainer: Monah Abou Alezz <aboualezz.monah@hsr.it>
Description: 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.
License: GPL (>= 3)
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
URL: https://github.com/monahton/GencoDymo2,
        https://monahton.github.io/GencoDymo2/
BugReports: https://github.com/monahton/GencoDymo2/issues
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)
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://monahton.r-universe.dev
Date/Publication: 2026-02-05 19:13:24 UTC
RemoteUrl: https://github.com/monahton/GencoDymo2
RemoteRef: main
RemoteSha: 98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27
NeedsCompilation: no
Packaged: 2026-09-21 11:49:42 UTC; root
Author: Monah Abou Alezz [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-2006-4250>),
  Lorenzo Salviati [ctb],
  Roberta Alfieri [ctb],
  Silvia Bione [ctb]