tlsR

CRAN status R-CMD-check

tlsR provides fast, reproducible detection and spatial analysis of Tertiary Lymphoid Structures (TLS) in multiplexed tissue imaging data (mIHC, CODEX, IMC, etc.).

Installation

# Stable release from CRAN
install.packages("tlsR")

# Development version from GitHub
# install.packages("remotes")
remotes::install_github("labsyspharm/tlsR")

Quick start

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)

Data format

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

Citation

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

License

MIT © Ali Amiryousefi