Package index • tlsR

TLS Detection

Identify tertiary lymphoid structures in spatial imaging data.

detect_TLS(): Detect Tertiary Lymphoid Structures using a KNN-density approach

T-cell Clusters

Detect tumour-infiltrating T-cell clusters outside TLS.

detect_tic(): Detect T-cell Immune Clusters (TIC) on the Tissue

Spatial Scanning

Sliding-window Ripley’s L clustering map.

scan_clustering(): Scan Tissue for Local Immune Cell Clustering (Ripley's L Heatmap)

Characterisation

Score and summarise detected structures.

calc_icat(): Calculate ICAT (Independent Component Analysis Trace) Index for TLS
summarize_TLS(): Summarize Detected TLS Across Samples

Visualisation

Publication-ready spatial plots.

plot_TLS(): Plot Spatial Map of TLS and T-cell Clusters

Data

Built-in example dataset.

toy_ldata: Toy Multiplexed Imaging Data

Package

Package-level documentation.

tlsR-package tlsR: tlsR: Detection and Spatial Analysis of Tertiary Lymphoid Structures