Software

SAIGE: SNP-set (Sequence) Kernel Association Test

SAIGE is an R-package for testing for associations between genetic variants and binary phenotypes 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. 

  • Github: link
  • For the UKBiobank analysis results, see Resources page

    SKAT: SNP-set (Sequence) Kernel Association Test

    SKAT is an R-package for rare variant association analysis. It can carry out burden test, SKAT, SKAT-O, and combined test 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.

    • Download (CRAN): link  
    • SKAT and MetaSKAT user group: link 
    • Github: link

    MetaSKAT: Meta-analysis for Rare Variants

    MetaSKAT is an R package for multiple marker meta-analysis across studies. It can carry out meta-analysis of SKAT, SKAT-O and burden tests with individual level genotype data or gene-level summary statistics.

    • Download (CRAN): link  
    • SKAT and MetaSKAT user group: link 
    • Github: link

    iECAT: integrating External Controls to Association Tests

    iECAT is an R-package to test for single variant and gene/region-based associations using external control samples. 

    • Download (CRAN): link  
    • Example dataset: link
    • Github: link

    SPAtest: Score Test Based on Saddlepoint Approximation

    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. 

    • Download (CRAN): link  

    dSVA: Direct Surrogate Variable Analysis

    dSVA is a R-package to identify hidden factors in high-dimensional biomedical data. 

    • Download (CRAN): link  

    TransMeta: Trans-ethnic Meta-analysis

    TransMeta is a R-package to compute single SNP p-values of trans-ethnic meta-analysis using a kernel based random effect model. You can download a package source from here (link). This is an early version, and we will keep updating it.   

    EigenCorr

    EigenCorr is a R-package to compute p-values of principal components (PCs) based on EigenCorr1, EigenCorr2 and Tracy-Widom methods. You need PCs, outcome phenotypes and all eigenvalues to run EigenCorr. 

    • Download package source: link  
    • Manual: link 

    Hapsample

    This is a command line version of Hapsample. Hapsampe is a simulation tool for generating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be "genotyped," along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans. (Currently, only the CEU database is available, so users cannot generate genotypes using YRI or JPT-CHN.)

    • Download package source: link  
    • Manual: link 
    • CEU database file: link 
    16
    Ċ
    Seunggeun Lee,
    Dec 1, 2014, 8:41 PM
    ċ
    EigenCorr_0.2.tar.gz
    (445k)
    Seunggeun Lee,
    Dec 1, 2014, 8:41 PM
    ċ
    SPAtest_1.0.0.tar.gz
    (4k)
    Seunggeun Lee,
    Feb 15, 2017, 1:30 PM
    ċ
    TransMeta_0.1.tar.gz
    (911k)
    Seunggeun Lee,
    Dec 15, 2014, 6:56 AM
    ċ
    dSVA_1.0.tar.gz
    (3758k)
    Seunggeun Lee,
    Oct 24, 2016, 9:53 AM
    ċ
    hapsample-0.12.tar.gz
    (426k)
    Seunggeun Lee,
    Jan 7, 2015, 7:18 AM
    ċ
    iECAT_0.8.tar.gz
    (232k)
    Seunggeun Lee,
    May 10, 2017, 7:44 AM
    ċ
    iECAT_Example.zip
    (89k)
    Seunggeun Lee,
    Jun 28, 2016, 10:25 AM
    ċ
    Seunggeun Lee,
    Jan 7, 2015, 7:18 AM
    Comments