Tutorials

The tutorial notebooks live in docs/tutorials/ and are committed with saved cell outputs; the documentation renders those outputs without re-executing the notebooks.

SNPObject

Read, inspect, filter, and manipulate SNP data.

Tutorial on SNPObj Functionalities

SNP PCA

Run PCA workflows on SNP data and inspect components.

Tutorial on PCA

Allele Frequency

Compute cohort and ancestry-aware allele frequencies.

SNPObject Allele Frequency Demo

Local Ancestry Visualization

Render local ancestry outputs at sample and dataset levels.

Tutorial on LAI Visualization

mdPCA and maasMDS

Use missing-data PCA and ancestry-specific MDS.

Tutorial on mdPCA and maasMDS Visualization

Admixture Mapping

Run the admixture-mapping pipeline and inspect its outputs.

Tutorial on admixture mapping

Phenotype Objects

Load and work with phenotype containers.

Tutorial on the MultiPhenotypeObject Functionalities

GRG

Work with genotype representation graph data.

GRG Demo