Detection and Spatial Analysis of Tertiary Lymphoid Structures R package tlsR version 0.3.0 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>. Software Depends: R (>= 4.0.0) Imports: dbscan (>= 1.1-10), fastICA (>= 1.2-3), FNN (>= 1.1.3), spatstat.explore (>= 3.0-0), spatstat.geom (>= 3.0-0), ggplot2 (>= 3.4.0), rlang (>= 1.0.0), grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, testthat (>= 3.0.0) Ali Amiryousefi <ali_amiryousefi@hms.harvard.edu> Comprehensive R Archive Network (CRAN) Ali Amiryousefi [aut, cre] (ORCID: <https://orcid.org/0000-0002-6317-3860>), Jeremiah Wala [aut] (ORCID: <https://orcid.org/0000-0001-6591-1620>), Peter Sorger [ctb] (ORCID: <https://orcid.org/0000-0002-3364-1838>) MIT + file LICENSE (https://CRAN.R-project.org/package=tlsR/LICENSE) 2026-04-23 application/tgz https://CRAN.R-project.org/package=tlsR doi:10.32614/CRAN.package.tlsR