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tlsR (version 0.1.2)

Detection and Spatial Analysis of Tertiary Lymphoid Structures

Description

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) .

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Version

Install

install.packages('tlsR')

Version

0.1.2

License

MIT + file LICENSE

Maintainer

Ali Amiryousefi

Last Published

December 18th, 2025

Functions in tlsR (0.1.2)

tlsR-package

tlsR: Detection and Spatial Analysis of Tertiary Lymphoid Structures
calc_icat

Calculate ICAT (Immune Cell Arrangement Trace) Index
scan_clustering

Scan Tissue for Local Immune Cell Clustering (K-integral)
detect_tic

Detect Tumor-Infiltrating T-cell Clusters (TIC)
detect_TLS

Detect Tertiary Lymphoid Structures using a KNN-density approach
toy_ldata

Toy multiplexed imaging data for examples