Package: GencoDymo2
Type: Package
Title: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs
Version: 1.0.2
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: 7.3.2
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