R Observatory: Metrics for tlsR version 0.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tlsR

0.3.0Package record

Detection and Spatial Analysis of Tertiary Lymphoid Structures

0packages depend

3.1Kdownloads / year

69.1%test coverage

13/13flavors OK

Overview

About

Maintained by Ali AmiryousefiCRAN page ↗GitHub ↗

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.

Changes in 0.3.0

Breaking changes

scan_clustering() — completely redesigned. The function no longer runs Monte Carlo CSR envelope tests. Instead it computes the **K-integral** clustering index (mean positive L excess over theoretical CSR) in each sliding window and — when plot = TRUE (now the default) — draws a spatial base-graphics map with LOESS-smoothed L-excess curves and numeric CI labels overlaid inside each qualifying window. The returned value is a plain list of Lest objects (one per qualifying window). The nsim argument has been removed; a new min_phen_cells argument controls the per-window phenotype-cell threshold.

Improvements to existing functions

calc_icat() — fixed sign-ambiguity bug. The previous implementation returned the raw signed trace of the FastICA mixing matrix, which could be negative. The index is now computed as 100 * sqrt(v1 + v2 + 2*sqrt(v1*v2)) / nrow(X) — a normalised trace-standard-deviation of the ICA-reconstructed coordinates — which is always non-negative and reflects average spatial spread per cell in microns.

Show all changes in 0.3.0Hide the rest of the changes in 0.3.0

plot_TLS() — two visual improvements:
Background (non-TLS, non-TIC) cells are now rendered with bg_alpha = 0.25 by default, making them more visually recessive.
TIC cells are drawn at point_size * tic_size_mult (default 1.8x), making them slightly larger than TLS cells.

Both new arguments (bg_alpha, tic_size_mult) are fully exposed.

Internal

NAMESPACE updated: added grDevices::adjustcolor, graphics::*, stats::cov, stats::loess, stats::predict; removed spatstat.explore::envelope (no longer needed).
DESCRIPTION Imports extended to declare grDevices, graphics, stats.
Vignette updated throughout to reflect all changes.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("tlsR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("labsyspharm/tlsR")

Development version from labsyspharm/tlsR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-tlsr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-tlsR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-tlsR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 6.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.0

READMEYes · 122 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.3.0Citation fileNo

Help pages: 8includes a package overview page
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 25%

Vignettes (1)

tlsR Workflow: From Raw Imaging Data to TLS Characterisation

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #10,813 · ~8/day · ~259/mo

Releases R versions

Daily download trend is not available in this view yet.

40430 days

97490 days

3.1K1 year

Compare downloads with other packages →

Also on66 r2u3 autocran

How downloads are counted

Repository

labsyspharm/tlsr ↗Organization: labsyspharm

0Stars

0Forks

2Open issues

0Open PRs

0Releases

License file reads as MIT · Last activity 2026-04-23

Responsiveness

not measured

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/labsyspharm/tlsr on 2026-10-21.

Docs source (1)

GitHub Pages site last deployed 2026-04-23

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing tlsR adds 34 packages (20 with compiled code, 24 MB of source tarballs). Heaviest: ggplot2 6.0 MB, dbscan 3.8 MB, spatstat.data 2.9 MB.

Depends (1)

R >= 4.0.0

Imports (11)

dbscan fastICA FNN spatstat.explore spatstat.geom ggplot2 rlanggrDevicesgraphicsstatsmethods

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Ali Amiryousefi

Author, Maintainer since 0.1.2 (2025)

Jeremiah Wala

Author

Peter Sorger

Contributor

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.3.0Latest
record
2026-04-23 · current release · diff ↗
0.2.0
record
2026-04-09 · diff ↗ ·
added 2 exports
plot_TLS, summarize_TLS
0.1.2
record
2025-12-18
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-12-18
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Bundled data: 754 KB / 1 file
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("tlsR")

Format

Amiryousefi, A., Sorger, P., & Wala, J. (2026). tlsR: Detection and Spatial Analysis of Tertiary Lymphoid Structures (Version 0.3.0) [Computer software]. https://doi.org/10.32614/CRAN.package.tlsR

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for tlsR version 0.3.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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