bioconda / packages / bioconductor-saigegds 1.2.0

Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies


conda install

  • linux-64  v1.2.0
  • osx-64  v1.2.0
To install this package with conda run:
conda install -c bioconda bioconductor-saigegds


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 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 original SAIGE R package (v0.29.4.4). SAIGEgds also implements some of the SPAtest functions in C to speed up the calculation of Saddlepoint approximation. Benchmarks show that SAIGEgds is 5 to 6 times faster than the original SAIGE R package.

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