Package: GRIN2
Title: Genomic Random Interval (GRIN)
Version: 2.1.0
Authors@R: 
    c(
      person(
        "Abdelrahman", "Elsayed",
        email = "aelsayed@stjude.org",
        role = c("aut", "cre", "cph"),
        comment = c(ORCID = "0000-0002-8150-6825")
      ),
      person(
        "Xueyuan", "Cao",
        email = "xcao12@uthsc.edu",
        role = "aut"
      ),
      person(
        "Lakshmi Anuhya", "Patibandla",
        email = "lakshmianuhya.patibandla@stjude.org",
        role = "aut"
      ),
      person(
        "Stanley", "Pounds",
        email = "stanley.pounds@stjude.org",
        role = c("aut", "cph")
      )
    )
Description: Implements the Genomic Random Interval (GRIN) framework for
    identifying genomic loci affected by genomic lesions more frequently than
    expected by chance. Supports multiple lesion classes, lesion constellation
    analysis, exon-level target-size modeling, genomic lesion visualization,
    and gene-level association analyses linking genomic lesions or gene
    expression with binary and time-to-event clinical outcomes. Includes tools
    for retrieving versioned GRCh38 Ensembl gene, exon, and regulatory-element
    annotations. The statistical framework is described in Pounds et al. (2013)
    <doi:10.1093/bioinformatics/btt372>.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.2.0)
Imports: circlize, data.table, dplyr, forcats, ggplot2, graphics,
        grDevices, grid, magrittr, stats, survival, tibble, tools,
        utils, writexl
Suggests: AnnotationHub, biomaRt, ComplexHeatmap, ensembldb,
        GenomeInfoDb, GenomicRanges, gridExtra, gridGraphics, Gviz,
        IRanges, knitr, rmarkdown, S4Vectors
VignetteBuilder: knitr, rmarkdown
LazyData: true
NeedsCompilation: no
Maintainer: Abdelrahman Elsayed <aelsayed@stjude.org>
URL: https://github.com/abdel-elsayed87/GRIN2
BugReports: https://github.com/abdel-elsayed87/GRIN2/issues
Config/roxygen2/markdown: TRUE
Config/roxygen2/version: 8.0.0
Packaged: 2026-08-22 04:34:08 UTC; aelsayed
Author: Abdelrahman Elsayed [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-8150-6825>),
  Xueyuan Cao [aut],
  Lakshmi Anuhya Patibandla [aut],
  Stanley Pounds [aut, cph]
Repository: CRAN
Date/Publication: 2026-08-22 15:20:20 UTC
Built: R 4.7.0; ; 2026-08-24 13:34:32 UTC; windows
