Package: cageminer
Title: Candidate Gene Miner
Version: 1.17.0
Authors@R: 
    c(
    person(given = "Fabrício",
           family = "Almeida-Silva",
           role = c("aut", "cre"),
           email = "fabricio_almeidasilva@hotmail.com",
           comment = c(ORCID = "0000-0002-5314-2964")),
    person(given = "Thiago",
           family = "Venancio",
           role = "aut",
           comment = c(ORCID = "0000-0002-2215-8082"))
    )
Description: This package aims to integrate GWAS-derived SNPs and coexpression
    networks to mine candidate genes associated with a particular phenotype.
    For that, users must define a set of guide genes, which are known genes 
    involved in the studied phenotype. Additionally, the mined candidates can
    be given a score that favor candidates that are hubs and/or transcription
    factors. The scores can then be used to rank and select the top n most
    promising genes for downstream experiments.
License: GPL-3
URL: https://github.com/almeidasilvaf/cageminer
BugReports: https://support.bioconductor.org/t/cageminer
biocViews: 
    Software,
    SNP,
    FunctionalPrediction,
    GenomeWideAssociation,
    GeneExpression,
    NetworkEnrichment,
    VariantAnnotation,
    FunctionalGenomics,
    Network
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports:
    ggplot2,
    rlang,
    ggbio,
    ggtext,
    GenomeInfoDb,
    GenomicRanges,
    IRanges,
    reshape2,
    methods,
    BioNERO
Depends: 
    R (>= 4.1)
Suggests: 
    testthat (>= 3.0.0),
    SummarizedExperiment,
    knitr,
    BiocStyle,
    rmarkdown,
    covr,
    sessioninfo
Config/testthat/edition: 3
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/cageminer
git_branch: devel
git_last_commit: b88d03b
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
