tlsR provides fast, reproducible detection and spatial analysis of Tertiary Lymphoid Structures (TLS) in multiplexed tissue imaging data (mIHC, CODEX, IMC, etc.).
# Stable release from CRAN
install.packages("tlsR")
# Development version from GitHub
# install.packages("remotes")
remotes::install_github("https://github.com/labsyspharm/tlsR/")library(tlsR)
data(toy_ldata)
# 1. Detect TLS
ldata <- detect_TLS("ToySample", k = 30, ldata = toy_ldata)
# 2. Score each TLS with ICAT
calc_icat("ToySample", tlsID = 1, ldata = ldata)
# 3. Detect T-cell clusters outside TLS
ldata <- detect_tic("ToySample", ldata = ldata)
# 4. Tidy summary table
summarize_TLS(ldata)
# 5. Spatial plot
plot_TLS("ToySample", ldata = ldata)ldata is a named list of data frames, one per sample, each with columns:
| Column | Type | Description |
|---|---|---|
x |
numeric | X coordinate (microns) |
y |
numeric | Y coordinate (microns) |
phenotype |
character | "B cell", "T cell", or other |
Amiryousefi et al. (2025). Detection and spatial analysis of tertiary lymphoid structures in multiplexed tissue imaging. https://doi.org/10.1101/2025.09.21.677465
MIT © Ali Amiryousefi