Package: tlsR
Type: Package
Title: Detection and Spatial Analysis of Tertiary Lymphoid Structures
Version: 0.3.0
Date: 2026-04-02
Authors@R: c(
    person("Ali", "Amiryousefi",
           email = "ali_amiryousefi@hms.harvard.edu",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-6317-3860")),
    person("Jeremiah", "Wala",
           email = "jeremiah_wala@dfci.harvard.edu",
           role = "aut",
           comment = c(ORCID = "0000-0001-6591-1620")),
    person("Peter", "Sorger",
           role = "ctb",
           comment = c(ORCID = "0000-0002-3364-1838")))
Description: 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>.
License: MIT + file LICENSE
URL: https://github.com/labsyspharm/tlsR
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)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-04-23 20:08:52 UTC; ali
Author: Ali Amiryousefi [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6317-3860>),
  Jeremiah Wala [aut] (ORCID: <https://orcid.org/0000-0001-6591-1620>),
  Peter Sorger [ctb] (ORCID: <https://orcid.org/0000-0002-3364-1838>)
Maintainer: Ali Amiryousefi <ali_amiryousefi@hms.harvard.edu>
Repository: CRAN
Date/Publication: 2026-04-23 20:40:02 UTC
Built: R 4.5.3; ; 2026-05-06 18:58:55 UTC; windows
