Documentation index

Choose a section according to the task. gsuite brings together seven public standalone R packages and native computational libraries. Mixed-model examples use the development integration; greml/gsolve R packaging is deferred. gsim and gact have their own public sites.

Start here

• Overview
• Tutorials: complete analyses
• Guides: individual methods and data preparation
• Software validation: focused simulation checks and limits
• Benchmarks: performance comparisons
• Presentations: slides and discussion

Standalone package tutorials

• Study design and reproducibility
• gbase: genotype and LD preparation
• glma: association analysis and VEGAS
• gbayes: Bayesian genomic regression
• gcorr: heritability and genetic correlation
• gmap: regional fine-mapping
• gscore: polygenic scoring
• gsea: genes and pathways

About gsuite

• Architecture and libraries
• Capabilities and R workflows
• Software availability
• Current status

Reference

• Standalone quick start
• Standalone installation and maintenance
• Standalone models and YAML examples
• Standalone results and diagnostics
• YAML model specification
• Standalone GenomeDK validation
• Mixed-model catalog
• Association analysis tutorial
• Association scan scope
• Model recipes
• Formulas and covariance components
• Persistent R interface
• Model representation
• Numerical routes
• Matrix integration

Other packages

• gsim documentation
• gact documentation