User guide#
Concepts behind AlphaGenome inputs, outputs, imputed tracks, and variant scoring.
Intervals, variants, prediction containers (TrackData, GeneExpressionData,
InputGradientsOutput), variant-score AnnData objects, and a glossary of core
terms.
Output types, units, resolutions, channels, and track metadata across AlphaGenome 2 and AlphaGenome 1.
What the observed, imputed_supported, and imputed_exploratory labels mean,
and pitfalls when using imputed tracks.
Spatial masks, indel alignment, and ALT - REF aggregation across scorers.
How plot_components.plot, track and expression components, enhancer arcs,
contact maps, and interval or variant annotations fit together.
API translation table, behavioral changes between AlphaGenome 1 and AlphaGenome 2, and when to use each model.