R Observatory: Metrics for netcutter version 0.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

netcutter

0.3.1

Identification and Analysis of Co-Occurrence Networks

0packages depend

5.7Kdownloads / year

94.6%test coverage

13/13checks pass

Overview

About

Maintained by Federico MarottaFirst published 2025-05-211 releasesCRAN page ↗GitHub ↗

Implementation of the NetCutter algorithm described in Müller and Mancuso (2008) doi:10.1371/journal.pone.0003178. The package identifies co-occurring terms in a list of containers. For example, it may be used to detect genes that co-occur across genomes.

Install

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

install.packages("netcutter", 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("fmarotta/netcutter")

Development version from fmarotta/netcutter. 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-netcutter

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-netcutter

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-netcutter

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

Health

CRAN checks

13OK

Slowest check: 1.8 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.51

94.6%

Coverage · measured lines

100%

Documentation · exports

2

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 255 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 93%
Return-value docs: 100%
References docs: 0%

Downloads

5.7K

CRAN downloads in the past year

Rank #9,607 · ~16/day · ~477/mo

Releases R versions

Daily download trend is not available in this view yet.

16830 days

97390 days

5.7K1 year

Compare downloads with other packages →

Also on102 r2u13 autocran

Repository

GitHub ↗ fmarotta/netcutter

0Stars

0Forks

0Open issues

0Open PRs

6Releases

35Commits

1Contributors

35 commits · Last activity 2025-05-30

Releases over time

2025-05-19 · 62026-07-07 · 6

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/fmarotta/netcutter on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (2)

PoissonBinomial rlecuyer

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown qpdf testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Federico Marotta

Maintainer

Authors (2)

Francesco Mancuso

Author

Heiko Müller

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.3.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-21
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 18 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("netcutter")

Format

Marotta, F., Mancuso, F., & Müller, H. (2025). netcutter: Identification and Analysis of Co-Occurrence Networks (Version 0.3.1) [Computer software]. https://doi.org/10.32614/CRAN.package.netcutter

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 netcutter version 0.3.1 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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