cageminer
R packages
bioconductor
networks
gene discovery
GWAS
An R/Bioconductor package to mine candidate genes by integrating GWAS and gene coexpression networks”
Summary
cageminer 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.