R Observatory: Metrics for LISTO version 0.8.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LISTO

0.8.1

Performing Comprehensive Overlap Assessments

0packages depend

2.1Kdownloads / year

86.6%test coverage

13/13checks pass

Overview

About

Maintained by Andrei-Florian StoicaFirst published 2026-03-063 releasesCRAN page ↗GitHub ↗

The implementation of a statistical framework for performing overlap assessments on lists comprising sets of strings (such as lists of gene sets) described in Stoica (2023) https://ora.ox.ac.uk/objects/uuid:b0847284-a02f-47ee-88e3-a3c4e0cdb8b1. It can assess overlaps of pairs of sets of strings selected either from the same universe or from different universes, and overlaps of triplets of sets of strings selected from the same universe. Designed for single-cell RNA-sequencing data analysis applications, but suitable for other purposes as well.

Install

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

install.packages("LISTO", 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("andrei-stoica26/LISTO")

Development version from andrei-stoica26/LISTO. 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-listo

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-LISTO

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-LISTO

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 6.7 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.22

86.6%

Coverage · measured lines

100%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
9 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 346 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.1K

CRAN downloads in the past year

Rank #8,042 · ~6/day · ~172/mo

Releases R versions

Daily download trend is not available in this view yet.

23930 days

1.1K90 days

2.1K1 year

Compare downloads with other packages →

Also on46 r2u22 autocran

Repository

GitHub ↗ andrei-stoica26/listo

2Stars

0Forks

0Open issues

0Open PRs

0Releases

91Commits

1Contributors

91 commits · Last activity 2026-07-13 · 0% stars, 30d

Stars over time

2026-04-25 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

Checks run against github.com/andrei-stoica26/listo on 2026-08-23.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (5)

methodsparallelprimes statisfactorystats

LinkingTo (0)

none

Suggests (6)

qs2 scRNAseq scuttle Seurat testthat withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Andrei-Florian Stoica

Author, Maintainer

Authors (1)

Andrei-Florian Stoica

Author, Maintainer

Package Timeline

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

0.8.1Latest
2026-07-13 · current release · diff ↗
0.7.3
2026-04-25 · diff ↗
R
R 4.6.0 released · 2026-04-24
0.6.5
2026-03-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-03-06
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 885 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("LISTO")

Format

Stoica, A. (2026). LISTO: Performing Comprehensive Overlap Assessments (Version 0.8.1) [Computer software]. https://doi.org/10.32614/CRAN.package.LISTO

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 LISTO version 0.8.1 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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