Package: SAIGEgds
Type: Package
Title: Scalable Implementation of Generalized mixed models using GDS
        files in Phenome-Wide Association Studies
Version: 2.13.0
Date: 2026-04-23
Depends: R (>= 4.0.0), gdsfmt (>= 1.28.0), SeqArray (>= 1.50.2), Rcpp
LinkingTo: Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0)
Imports: methods, stats, utils, Matrix, RcppParallel, SKAT,
        CompQuadForm, survey
Suggests: parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit,
        knitr, ggmanh, BiocGenerics
Authors@R: c(person("Xiuwen", "Zheng", role=c("aut", "cre"),
        email="xiuwen.zheng@abbvie.com", comment=c(ORCID="0000-0002-1390-0708")),
        person("Wei", "Zhou", role="ctb",
        comment="the original author of the SAIGE R package"),
        person("J. Wade", "Davis", role="ctb"))
Description: Scalable implementation of generalized mixed models with
        highly optimized C++ implementation and integration with
        Genomic Data Structure (GDS) files. It is designed for single
        variant tests and set-based aggregate tests in large-scale
        Phenome-wide Association Studies (PheWAS) with millions of
        variants and samples, controlling for sample structure and
        case-control imbalance. The implementation is based on the
        SAIGE R package (v0.45, Zhou et al. 2018 and Zhou et al. 2020),
        and it is extended to include the state-of-the-art ACAT-O
        set-based tests. Benchmarks show that SAIGEgds is significantly
        faster than the SAIGE R package. Optional OpenCL-based GPU
        acceleration is supported for the GRM cross-product computation
        in null model fitting and for GRM construction.
License: GPL-3
SystemRequirements: GNU make
VignetteBuilder: knitr
ByteCompile: TRUE
URL: https://github.com/AbbVie-ComputationalGenomics/SAIGEgds
biocViews: Software, Genetics, StatisticalMethod, GenomeWideAssociation
Config/pak/sysreqs: make zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:51:06 UTC
RemoteUrl: https://github.com/bioc/SAIGEgds
RemoteRef: HEAD
RemoteSha: e2f4a5f55cb001e1471fae0fb6fb2fd09d41826c
NeedsCompilation: yes
Packaged: 2026-07-05 09:37:12 UTC; root
Author: Xiuwen Zheng [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1390-0708>),
  Wei Zhou [ctb] (the original author of the SAIGE R package),
  J. Wade Davis [ctb]
Maintainer: Xiuwen Zheng <xiuwen.zheng@abbvie.com>