TarGene is a Nextflow pipeline for the estimation of genetic effects on human traits using highly flexible semi-parametric inference methods (Targeted Minimum Loss-Based Estimation, One-Step Estimation).
If you would like to use flexible machine-learning methods while preserving valid statistical inference and your project falls within any of the following, then the answer is Yes!
Supported study designs:
- GWAS
- PheWAS
- Custom
Supported databases:
- UK Biobank
- All of Us
- Custom
Supported genetic effects:
- Main effects
- Interactions up to any order
Want to know more? Please visit the docs.
TarGene is a Nextflow pipeline, please refer to their documentation for general usage. The main point being that, depending on your HPC specifications, you will need to provide a specific myplatform.config configuration file on top of your project myproject.config configuration file.
nextflow run TARGENE/targene-pipeline -c myplatform.config -c myproject.config -resume