Bioconductor: https://bioconductor.org/packages/release/bioc/html/rqt.html
Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R package rqt offers gene-level GWAS meta-analysis.
References:
- Zhbannikov I., Arbeev K., and Yashin A. (2017) rqt: an R package for gene-level meta-analysis. Bioinformatics 33(19):3129–3130. [ doi: 10.1093/bioinformatics/btx395 ] [ PMID: 28633423 ]
- Lee J. et al. (2016) Gene-set association tests for next-generation sequencing data. Bioinformatics 32(17):i611-i619. [ doi:10.1093/bioinformatics/btw429 ] [ PMID: 27587681 ] [ PMCID: PMC5013913 ]
