Tutorials

End-to-end notebooks for data objects, population structure, ancestry visualization, association testing, and GRG workflows. Examples use synthetic or registered downloadable datasets unless a notebook states otherwise.

SNPObject

Read, inspect, filter, and manipulate SNP data.

SNPObject

PCA

Run PCA workflows on SNP data and inspect components.

Run population-genetics PCA in Python

Allele Frequency

Compute cohort and ancestry-aware allele frequencies.

SNP Allele Frequency

F-statistics

Compute f-statistics, D-statistics, f4-ratios, and F_ST.

Calculate FST and f-statistics in Python

Local Ancestry Visualization

Render local ancestry outputs at sample and dataset levels.

Local ancestry analysis and visualization in Python

mdPCA

Recover population structure under high genotype missingness.

Missing-data PCA (mdPCA)

maasMDS

Calibrate distances across multiple genotyping arrays.

Multi-array ancestry-specific Multidimensional Scaling (maasMDS)

Admixture Mapping

Run the admixture-mapping pipeline and inspect its outputs.

Run admixture mapping from local ancestry

Phenotype Objects

Load and work with phenotype containers.

Phenotype Objects

GRG

Work with genotype representation graph data.

Genotype Representation Graphs (GRG)