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>.

Version: 0.2.0
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), methods
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
Published: 2026-04-09
DOI: 10.32614/CRAN.package.tlsR
Author: Ali Amiryousefi ORCID iD [aut, cre], Jeremiah Wala ORCID iD [aut], Peter Sorger ORCID iD [ctb]
Maintainer: Ali Amiryousefi <ali_amiryousefi at hms.harvard.edu>
License: MIT + file LICENSE
URL: https://github.com/labsyspharm/tlsR
NeedsCompilation: no
Materials: NEWS
CRAN checks: tlsR results

Documentation:

Reference manual: tlsR.html , tlsR.pdf
Vignettes: tlsR Workflow: From Raw Imaging Data to TLS Characterisation (source, R code)

Downloads:

Package source: tlsR_0.2.0.tar.gz
Windows binaries: r-devel: tlsR_0.2.0.zip, r-release: tlsR_0.1.2.zip, r-oldrel: tlsR_0.1.2.zip
macOS binaries: r-release (arm64): tlsR_0.1.2.tgz, r-oldrel (arm64): tlsR_0.1.2.tgz, r-release (x86_64): tlsR_0.2.0.tgz, r-oldrel (x86_64): tlsR_0.2.0.tgz
Old sources: tlsR archive

Linking:

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