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Software
SAIGE
SAIGE is an R-package for GWAS and rare-variant test with adjusting for sample relatedness and case-control imbalance. It can analyze very large sample data (ex. ~400,000 samples in UKBiobank) and produce accurate p-values by using saddlepoint approximation.
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Github: link
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For the UKBiobank analysis results, see Resources page
SKAT
SKAT is an R-package for rare variant association analysis. It can carry out burden tests, SKAT, SKAT-O, and combined tests of common and rare variants with adjusting for covariates and kinship. For binary traits, it can calculate p-values using resampling and asymptotic-based adjustment methods. It also has functions for sample size and power calculations.
SPAtest
SPAtest is an R-package to perform score test for associations between genetic variants and binary traits using saddlepoint approximation. The methods implemented in the package (FastSPA) can accurately calculate p-values even when the case-control ratio is extremely unbalanced.
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Download (CRAN): link
JointScoreTest
JointScoreTest is an R-package to perform a joint test of fixed and random effects in the Generalized linear mixed model framework.
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Download Package Source: link
TransMeta & TransMetaRare
TransMeta is an R-package to compute single SNP p-values of trans-ethnic meta-analysis using a kernel-based random effect model. This is an early version, and we will keep updating it. We have recently extended it to gene-based rare-variant test (Transmeta-rare). The packages can be downloaded from the following github.
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