Detection and Spatial Analysis of Tertiary Lymphoid Structures
Calculate ICAT (Immune Cell Arrangement Trace) Index
Detect Tumor-Infiltrating T-cell Clusters (TIC)
Detect Tertiary Lymphoid Structures using a KNN-density approach
Scan Tissue for Local Immune Cell Clustering (K-integral)
tlsR: Detection and Spatial Analysis of Tertiary Lymphoid Structures
Fast, reproducible detection and quantitative analysis of tertiary lymphoid structures (TLS) in multiplexed tissue imaging. Implements Independent Component Analysis Trace (ICAT) index, local Ripley's K scanning, automated K Nearest Neighbor (KNN)-based TLS detection, and T-cell clusters identification as described in Amiryousefi et al. (2025) <doi:10.1101/2025.09.21.677465>.