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: 0.1.2
Depends: R (≥ 3.5)
Imports: fastICA, spatstat.geom, spatstat.explore, dbscan, RANN, grDevices, graphics, stats, utils
Suggests: testthat (≥ 3.0.0)
Published: 2025-12-18
DOI: 10.32614/CRAN.package.tlsR (may not be active yet)
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
NeedsCompilation: no
Materials: NEWS
CRAN checks: tlsR results

Documentation:

Reference manual: tlsR.html , tlsR.pdf

Downloads:

Package source: tlsR_0.1.2.tar.gz
Windows binaries: r-devel: tlsR_0.1.2.zip, r-release: not available, r-oldrel: tlsR_0.1.2.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): tlsR_0.1.2.tgz, r-oldrel (x86_64): tlsR_0.1.2.tgz

Linking:

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