tlsR

tlsR-package

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) tools:::Rd_expr_doi("10.1101/2025.09.21.677465").

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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>.

Ali Amiryousefi

Detection and Spatial Analysis of Tertiary Lymphoid Structures

Jeremiah Wala

Peter Sorger

tlsR-package function

Maintainer: Ali Amiryousefi <a href="/link/ali_amiryousefi%40hms.harvard.edu?package=tlsR&version=0.1.2" data-mini-rdoc="tlsR::ali_amiryousefi@hms.harvard.edu">ali_amiryousefi@hms.harvard.edu</a> (<a href="https://orcid.org/0000-0002-6317-3860">ORCID</a>)
Authors:<ul>
<li>Jeremiah Wala <a href="/link/jeremiah_wala%40dfci.harvard.edu?package=tlsR&version=0.1.2" data-mini-rdoc="tlsR::jeremiah_wala@dfci.harvard.edu">jeremiah_wala@dfci.harvard.edu</a> (<a href="https://orcid.org/0000-0001-6591-1620">ORCID</a>)</li>
</ul>Other contributors:<ul>
<li>Peter Sorger (<a href="https://orcid.org/0000-0002-3364-1838">ORCID</a>) [contributor]</li>
</ul>

Author

tlsR: Detection and Spatial Analysis of Tertiary Lymphoid Structures — tlsR-package

Maintainer: Ali Amiryousefi <a href='mailto:ali_amiryousefi@hms.harvard.edu'>ali_amiryousefi@hms.harvard.edu</a> (<a href='https://orcid.org/0000-0002-6317-3860'>ORCID</a>)
Authors:<ul>
<li>Jeremiah Wala <a href='mailto:jeremiah_wala@dfci.harvard.edu'>jeremiah_wala@dfci.harvard.edu</a> (<a href='https://orcid.org/0000-0001-6591-1620'>ORCID</a>)</li>
</ul>

Other contributors:<ul>
<li>Peter Sorger (<a href='https://orcid.org/0000-0002-3364-1838'>ORCID</a>) [contributor]</li>
</ul>

tlsR-package: tlsR: Detection and Spatial Analysis of Tertiary Lymphoid Structures

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