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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "SAIGEgds" in publications use:'
type: software
license: GPL-3.0-only
title: 'SAIGEgds: Scalable Implementation of Generalized mixed models using GDS files
  in Phenome-Wide Association Studies'
version: 2.5.0
doi: 10.1093/bioinformatics/btaa731
abstract: 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.
authors:
- family-names: Zheng
  given-names: Xiuwen
  email: xiuwen.zheng@abbvie.com
  orcid: https://orcid.org/0000-0002-1390-0708
preferred-citation:
  type: generic
  title: SAIGEgds -- an efficient statistical tool for large-scale PheWAS with mixed
    models
  authors:
  - family-names: Zheng
    given-names: Xiuwen
    email: xiuwen.zheng@abbvie.com
    orcid: https://orcid.org/0000-0002-1390-0708
  - family-names: Davis
    given-names: J. Wade
  journal: Bioinformatics
  year: '2021'
  doi: 10.1093/bioinformatics/btaa731
repository: https://bioc.r-universe.dev
repository-code: https://github.com/AbbVie-ComputationalGenomics/SAIGEgds
url: https://github.com/AbbVie-ComputationalGenomics/SAIGEgds
date-released: '2024-04-17'
contact:
- family-names: Zheng
  given-names: Xiuwen
  email: xiuwen.zheng@abbvie.com
  orcid: https://orcid.org/0000-0002-1390-0708
references:
- type: article
  title: Efficiently controlling for case-control imbalance and sample relatedness
    in large-scale genetic association studies
  authors:
  - family-names: Zhou
    given-names: Wei
  - family-names: Nielsen
    given-names: Jonas B.
  - family-names: Fritsche
    given-names: Lars G.
  - family-names: Dey
    given-names: Rounak
  - family-names: Gabrielsen
    given-names: Maiken E.
  - family-names: Wolford
    given-names: Brooke N.
  - family-names: LeFaive
    given-names: Jonathon
  - family-names: VandeHaar
    given-names: Peter
  - family-names: Gagliano
    given-names: Sarah A.
  - family-names: Gifford
    given-names: Aliya
  - family-names: Bastarache
    given-names: Lisa A.
  - family-names: Wei
    given-names: Wei-Qi
  - family-names: Denny
    given-names: Joshua C.
  - family-names: Lin
    given-names: Maoxuan
  - family-names: Hveem
    given-names: Kristian
  - family-names: Kang
    given-names: Hyun Min
  - family-names: Abecasis
    given-names: Goncalo R.
  - family-names: Willer
    given-names: Cristen J.
  - family-names: Lee
    given-names: Seunggeun
  journal: Nature Genetics
  year: '2018'
  doi: 10.1038/s41588-018-0184-y
- type: article
  title: SeqArray -- A storage-efficient high-performance data format for WGS variant
    calls
  authors:
  - family-names: Zheng
    given-names: Xiuwen
  - family-names: Gogarten
    given-names: Stephanie
  - family-names: Lawrence
    given-names: Michael
  - family-names: Stilp
    given-names: Adrienne
  - family-names: Conomos
    given-names: Matthew
  - family-names: Weir
    given-names: Bruce
  - family-names: Laurie
    given-names: Cathy
  - family-names: Levine
    given-names: David
  journal: Bioinformatics
  year: '2017'
  doi: 10.1093/bioinformatics/btx145