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This is the development version of cageminer; for the stable release version, see cageminer.

Candidate Gene Miner

Bioconductor version: Development (3.20)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Mining high-confidence candidate genes with cageminer HTML R Script
Reference Manual PDF


biocViews FunctionalGenomics, FunctionalPrediction, GeneExpression, GenomeWideAssociation, Network, NetworkEnrichment, SNP, Software, VariantAnnotation
Version 1.11.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1)
Imports ggplot2, rlang, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO
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Suggests testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo
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Follow Installation instructions to use this package in your R session.

Source Package cageminer_1.11.0.tar.gz
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macOS Binary (x86_64) cageminer_1.11.0.tgz
macOS Binary (arm64) cageminer_1.11.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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