R Observatory: Metrics for tlsR version 0.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tlsR

0.3.0

Detection and Spatial Analysis of Tertiary Lymphoid Structures

0packages depend

2.3Kdownloads / year

69.1%test coverage

13/13checks pass

Overview

About

Maintained by Ali AmiryousefiFirst published 2025-12-183 releasesCRAN 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.

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.

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).

Health

CRAN checks

13OK

Slowest check: 5.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.26

69.1%

Coverage · measured lines

100%

Documentation · exports

11

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 122 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 25%

Downloads

2.3K

CRAN downloads in the past year

Rank #9,768 · ~6/day · ~188/mo

Releases R versions

Daily download trend is not available in this view yet.

18630 days

97190 days

2.3K1 year

Compare downloads with other packages →

Also on61 r2u18 autocran

Repository

GitHub ↗ labsyspharm/tlsr

0Stars

0Forks

2Open issues

0Open PRs

0Releases

License MIT · Last activity 2026-04-23

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/labsyspharm/tlsr on 2026-08-16.

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (3)

Maintainer (1)

Ali Amiryousefi

Author, Maintainer

Authors (2)

Ali Amiryousefi

Author, Maintainer

Jeremiah Wala

Author

Contributors (1)

Peter Sorger

Contributor

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

0.3.0Latest
2026-04-24 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.2.0
2026-04-09 · diff ↗
0.1.2
2026-03-10
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
Installed size: not tracked yet
With dependencies: not tracked yet

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 is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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