recipe bioconductor-saigegds

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

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/SAIGEgds.html

License:

GPL-3

Recipe:

/bioconductor-saigegds/meta.yaml

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.

package bioconductor-saigegds

versions:

2.2.0-0,  2.0.1-0,  1.12.0-1,  1.12.0-0,  1.8.1-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-1, 

2.2.0-0,  2.0.1-0,  1.12.0-1,  1.12.0-0,  1.8.1-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-gdsfmt:

>=1.38.0,<1.39.0

depends bioconductor-gdsfmt:

>=1.38.0,<1.39.0a0

depends bioconductor-seqarray:

>=1.42.0,<1.43.0

depends bioconductor-seqarray:

>=1.42.0,<1.43.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-matrix:

depends r-rcpp:

depends r-rcpparmadillo:

depends r-rcppparallel:

>=5.0.0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-saigegds

and update with::

   mamba update bioconductor-saigegds

To create a new environment, run:

mamba create --name myenvname bioconductor-saigegds

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-saigegds:<tag>

(see `bioconductor-saigegds/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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