Changelog

Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

0.1.0#

Added#

  • Atlas mapping via scArches surgery (tl.extend_atlas) and fast embed-only label transfer (tl.embed_and_predict).

  • Hierarchical MLP classifier (tl.predict_labels, HierarchicalClassifier) splitting malignant vs non-malignant before fine-grained typing.

  • Gene-panel alignment and quantile binning (pp.get_genes, pp.align_to_genes, pp.bin_data, pp.slice_and_bin) with manual human/mouse panels.

  • Pretrained human and mouse SCANVI models and classifier checkpoints, with models.load_scanvi_model and models.load_classifier_checkpoints.

  • Label-distribution plot (pl.plot_label_distribution).

  • Training, conversion and SLURM scripts, plus tutorial notebooks and a performance benchmark page.

Changed#

  • Load reference SCANVI models with scArches load_query_data.

  • Made internal modules private (_basic, _binning, _genes).

Removed#

  • Placeholder basic tool and example notebook.