User Guide¶
The user guide groups the library by workflow rather than by module path. Each page stands alone, but the sections below follow a typical analysis order.
Recommended reading order¶
Data Model — Object shapes, attributes, and filtering before you load real data.
File I/O — Format dispatch, reader/writer options, and synthetic datasets for experiments.
Analysis — Dimensionality reduction, allele frequencies, f-statistics, GWAS, admixture mapping, simulation, and the CLI.
Visualization — Scatter, local ancestry, admixture, Manhattan, and Q–Q plots.
After the quickstart, open the Tutorials notebooks for end-to-end examples with saved outputs.
SNPObject, LocalAncestryObject, GlobalAncestryObject, IBDObject, phenotype containers, and GRG.
Readers and writers for genotype, ancestry, phenotype, and IBD formats.
PCA, mdPCA, maasMDS, f-statistics, GWAS, admixture mapping, simulation, and CLI workflows.
Embedding scatter plots, chromosome painting, admixture bars, Manhattan, and Q–Q plots.