cran. To fix this you can add URL: https://cran.r-universe.dev/tlsR to the package DESCRIPTION file. See also theR-universe documentation.Package: tlsR 0.3.0
Ali Amiryousefi
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>.
Authors:
tlsR_0.3.0.tar.gz
tlsR_0.3.0.tar.gz(r-4.7-any)tlsR_0.3.0.tar.gz(r-4.6-any)
tlsR_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
tlsR/json (API)
NEWS
| # Install 'tlsR' in R: |
| install.packages('tlsR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/labsyspharm/tlsr/issues
- toy_ldata - Toy Multiplexed Imaging Data
Last updated from:b0b0fc313d. Checks:4 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 191 | ||
| source / vignettes | OK | 219 | ||
| linux-release-x86_64 | OK | 190 | ||
| wasm-release | OK | 109 |
Exports:calc_icatdetect_ticdetect_TLSplot_TLSscan_clusteringsummarize_TLS
Dependencies:abindclicpp11dbscandeldirfarverfastICAFNNgenericsggplot2gluegoftestgtableisobandlabelinglatticelifecycleMatrixnlmepolyclipR6RColorBrewerRcpprlangS7scalesspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilstensorvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| tlsR: Detection and Spatial Analysis of Tertiary Lymphoid Structures | tlsR-package tlsR |
| Calculate ICAT (Independent Component Analysis Trace) Index for TLS | calc_icat |
| Detect T-cell Immune Clusters (TIC) on the Tissue | detect_tic |
| Detect Tertiary Lymphoid Structures using a KNN-density approach | detect_TLS |
| Plot Spatial Map of TLS and T-cell Clusters | plot_TLS |
| Scan Tissue for Local Immune Cell Clustering (Ripley's L Heatmap) | scan_clustering |
| Summarize Detected TLS Across Samples | summarize_TLS |
| Toy Multiplexed Imaging Data | toy_ldata |
