DOI: 10.18129/B9.bioc.cageminer  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see cageminer.

Candidate Gene Miner

Bioconductor version: 3.16

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.

Author: Fabrício Almeida-Silva [aut, cre] , Thiago Venancio [aut]

Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at>

Citation (from within R, enter citation("cageminer")):


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biocViews FunctionalGenomics, FunctionalPrediction, GeneExpression, GenomeWideAssociation, Network, NetworkEnrichment, SNP, Software, VariantAnnotation
Version 1.4.0
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License GPL-3
Depends R (>= 4.1)
Imports ggplot2, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO
Suggests testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo
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