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 [aut, cre], Jeremiah Wala [aut], Peter Sorger [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): tlsR_0.1.2.tgz, r-oldrel (arm64): tlsR_0.1.2.tgz, r-release (x86_64): tlsR_0.1.2.tgz, r-oldrel (x86_64): tlsR_0.1.2.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=tlsR to link to this page.