omicverse-reference-label-transfer

What problem does it solve?

Label-transfer between AnnData objects is essential for applying reference annotations to new single-cell datasets. This skill enables transferring cell-type labels from a well-annotated reference to a query dataset by building a shared integrated space and using a weighted kNN transfer model.

Core Features & Use Cases

• Supports multiple backends (harmony, scVI, scanorama) to perform label transfer across integrated spaces.
• Provides a unified interface through AnnotationRef: preprocess, train, and predict, plus a batch_correction helper for preprocessing and validation.
• Use cases include annotating a new dataset with a reference, benchmarking transfer strategies, and reusing reference annotations in downstream analyses.

Quick Start

Prepare paired query and reference AnnData objects and run the harmony transfer path to generate predictions.