Tools: tl

This module provides various tools for analyzing proteomics data.

Clustering

tl.leiden_mito_sweep	Automated sweep to pick a Leiden resolution that keeps mitochondria intact.
tl.knn_annotation	Propagate categorical annotations along the k-NN graph.
tl.calculate_interfacialness_score	Quantify interfacialness of proteins across compartment boundaries.
tl.silhouette_score	Per-group silhouette scores.
tl.calinski_habarasz_score	Calinski–Harabasz score of cluster compactness vs separation.
tl.tagm_map_train	Train a TAGM-MAP (T-Augmented Gaussian Mixture, MAP variant) model.
tl.tagm_map_predict	Predict sub-cellular localization for unlabelled proteins using a fitted TAGM-MAP model.

Ontology Enrichment

tl.calculate_cluster_enrichment

Gene-set enrichment for each cluster.

Integration

tl.align_adatas	Return copies of several AnnData objects with matching index/columns.
tl.aligned_umap	Aligned UMAP embedding for matched datasets.
tl.remodeling_score	Compute per-protein remodeling score from two aligned datasets.

Graph analysis

tl.to_knn_graph	Convert the k-NN graph stored in AnnData to a networkx graph.
tl.get_n_nearest_neighbors	Return the set of closest neighbours for a node in a graph.