Package: cageminer
Title: Candidate Gene Miner
Version: 1.16.0
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
Config/pak/sysreqs: libglpk-dev make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libxml2-dev libssl-dev perl xz-utils
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:10:52 UTC
RemoteUrl: https://github.com/bioc/cageminer
RemoteRef: RELEASE_3_22
RemoteSha: 304c1d00bb3245ecd61019cb6be7f9f092a01f27
NeedsCompilation: no
Packaged: 2026-01-24 20:42:40 UTC; root
Author: Fabrício Almeida-Silva [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5314-2964>),
  Thiago Venancio [aut] (ORCID: <https://orcid.org/0000-0002-2215-8082>)
Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva@hotmail.com>
Built: R 4.5.2; ; 2026-01-24 21:04:55 UTC; unix
