R Observatory: Metrics for PLEXI version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PLEXI

1.0.0Package record

Multiplex Network Analysis

0packages depend

2.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Behnam YousefiCRAN page ↗

Interactions between different biological entities are crucial for the function of biological systems. In such networks, nodes represent biological elements, such as genes, proteins and microbes, and their interactions can be defined by edges, which can be either binary or weighted. The dysregulation of these networks can be associated with different clinical conditions such as diseases and response to treatments. However, such variations often occur locally and do not concern the whole network. To capture local variations of such networks, we propose multiplex network differential analysis (MNDA). MNDA allows to quantify the variations in the local neighborhood of each node (e.g. gene) between the two given clinical states, and to test for statistical significance of such variation. Yousefi et al. (2023) doi:10.1101/2023.01.22.525058.

Install

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

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

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

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-plexi

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-PLEXI

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-PLEXI

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: 1.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 21
Examples that run: 100%21 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

How these are measured

Downloads

2.1K

CRAN downloads in the past year

Rank #22,619 · ~6/day · ~173/mo

Releases R versions

Daily download trend is not available in this view yet.

22330 days

57990 days

2.1K1 year

Compare downloads with other packages →

Also on62 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing PLEXI adds 67 packages (38 with compiled code, 56 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.

Depends (0)

none

Imports (8)

assertthat igraph keras ggraph ggplot2 aggregationstatsgraphics

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Behnam Yousefi

Farzaneh Firoozbakht

Author

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.0Latest
record
2023-08-09 · current release
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-08-09
Total releases: 1 / 3 yrs
License: GPL (>= 3) OSI
Download size: 17 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PLEXI")

Format

Yousefi, B., & Firoozbakht, F. (2023). PLEXI: Multiplex Network Analysis (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.PLEXI

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 PLEXI version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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