Package: compSPOT
Type: Package
Title: compSPOT: Tool for identifying and comparing significantly
        mutated genomic hotspots
Version: 1.8.0
Authors@R: c(
    person("Sydney", "Grant", email = "Sydney.Grant@roswellpark.org", 
    role = c("aut", "cre"), 
    comment = c(ORCID = "0000-0003-1849-5921")),
    person("Ella", "Sampson", email = "ellasamp@buffalo.edu", role = c("aut")),
    person("Rhea", "Rodrigues", 
    email = "RheaCarmelGlen.Rodrigues@roswellpark.org", 
    role = c("aut"), comment = c(ORCID = "0000-0002-8573-8658")),
    person("Gyorgy", "Paragh", email = "Gyorgy.Paragh@roswellpark.org", 
    role = c("aut"), comment = c(ORCID = "0000-0002-6612-9267")))
Description: Clonal cell groups share common mutations within cancer, precancer, 
    and even clinically normal appearing tissues. The frequency and location of 
    these mutations may predict prognosis and cancer risk. It has also been well 
    established that certain genomic regions have increased sensitivity to 
    acquiring mutations. Mutation-sensitive genomic regions may therefore serve 
    as markers for predicting cancer risk. This package contains multiple 
    functions to establish significantly mutated hotspots, compare hotspot 
    mutation burden between samples, and perform exploratory data analysis of 
    the correlation between hotspot mutation burden and personal risk factors 
    for cancer, such as age, gender, and history of carcinogen exposure. This 
    package allows users to identify robust genomic markers to help establish 
    cancer risk.
License: Artistic-2.0
Encoding: UTF-8
LazyData: FALSE
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: Software, Technology, Sequencing, DNASeq, WholeGenome,
        Classification, SingleCell, Survival, MultipleComparison
Imports: stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra,
        utils, data.table
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/sydney-grant/compSPOT
BugReports: https://github.com/sydney-grant/compSPOT/issues
Config/testthat/edition: 3
Depends: R (>= 4.3.0)
git_url: https://git.bioconductor.org/packages/compSPOT
git_branch: RELEASE_3_22
git_last_commit: 762cc92
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 03:16:13 UTC; biocbuild
Author: Sydney Grant [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1849-5921>),
  Ella Sampson [aut],
  Rhea Rodrigues [aut] (ORCID: <https://orcid.org/0000-0002-8573-8658>),
  Gyorgy Paragh [aut] (ORCID: <https://orcid.org/0000-0002-6612-9267>)
Maintainer: Sydney Grant <Sydney.Grant@roswellpark.org>
