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: |
0.3.0 |
| 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), grDevices, graphics, stats, methods |
| Suggests: |
knitr, rmarkdown, testthat (≥ 3.0.0) |
| Published: |
2026-04-23 |
| DOI: |
10.32614/CRAN.package.tlsR |
| Author: |
Ali Amiryousefi 
[aut, cre],
Jeremiah Wala
[aut],
Peter Sorger
[ctb] |
| Maintainer: |
Ali Amiryousefi <ali_amiryousefi at hms.harvard.edu> |
| License: |
MIT + file LICENSE |
| URL: |
https://github.com/labsyspharm/tlsR |
| NeedsCompilation: |
no |
| Materials: |
README, NEWS |
| CRAN checks: |
tlsR results |
Documentation:
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