multiDEGGs

1.2.1

Multi-Omic Differentially Expressed Gene-Gene Pairs

0packages depend

4.1Kdownloads / year

43.5%test coverage

13/13checks pass

Overview

About

Maintained by Elisabetta SciaccaFirst published 2025-06-057 releasesCRAN page ↗GitHub ↗

Performs multi-omic differential network analysis by revealing differential interactions between molecular entities (genes, proteins, transcription factors, or other biomolecules) across the omic datasets provided. For each omic dataset, a differential network is constructed where links represent statistically significant differential interactions between entities. These networks are then integrated into a comprehensive visualization using distinct colors to distinguish interactions from different omic layers. This unified display allows interactive exploration of cross-omic patterns, such as differential interactions present at both transcript and protein levels. For each link, users can access differential statistical significance metrics (p values or adjusted p values, calculated via robust or traditional linear regression with interaction term) and differential regression plots. The methods implemented in this package are described in Sciacca et al. (2023) doi:10.1093/bioinformatics/btad192.

Install

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

install.packages("multiDEGGs", 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("elisabettasciacca/multiDEGGs")

Development version from elisabettasciacca/multiDEGGs. 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-multideggs

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-multiDEGGs

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-multiDEGGs

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

Health

CRAN checks

13OK

Slowest check: 4.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.18

43.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-16
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-31
12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 220 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

4.1K

CRAN downloads in the past year

Rank #7,933 · ~11/day · ~344/mo

Releases R versions

Daily download trend is not available in this view yet.

30130 days

1.4K90 days

4.1K1 year

Compare downloads with other packages →

Also on142 r2u13 autocran

Repository

GitHub ↗ elisabettasciacca/multideggs

8Stars

1Forks

0Open issues

1Open PRs

6Releases

168Commits

3Contributors

bioinformaticsdifferential-expressioninteractive-visualizationsmultiomicsmultiomics-datanetwork-analysisomicsproteomics

License GPL-3.0 · 168 commits · Last activity 2026-06-16 · 0% stars, 30d

Stars over time

2025-10-09 · 12026-07-07 · 8

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/elisabettasciacca/multideggs on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4.0

Imports (17)

DTgrDevicesgraphicsknitrMASSmagrittrmethodsparallelpbapply pbmcapply rmarkdown sfsmisc shiny shinydashboardstatsutilsvisNetwork

LinkingTo (0)

none

Suggests (7)

kernlab nestedcv pls qvalue randomForest ranger testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Elisabetta Sciacca

Author, Maintainer, Copyright holder

Authors (1)

Elisabetta Sciacca

Author, Maintainer, Copyright holder

Contributors (1)

Myles Lewis

Contributor

Elisabetta Sciacca

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2.1Latest
2026-04-10 · current release · diff ↗
1.2.0
2026-03-24 · diff ↗
1.1.3
2026-02-02 · diff ↗
1.1.2
2026-01-16 · diff ↗
1.1.1
2025-10-24 · diff ↗
unarchivedReturned to CRAN
2025-10-24
archivedRemoved from CRAN
2025-10-23
check issues were not corrected in time
1.1.0
2025-07-29 · diff ↗
1.0.0
2025-06-05
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-06-05
Total releases: 7 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.4.0
Bundled data: 21 KB / 4 files
Download size: 3.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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