R Observatory: Metrics for difconet version 1.0-4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

difconet

1.0-4

Differential Coexpressed Networks

0packages depend

2.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Victor TrevinoFirst published 2017-05-311 releasesCRAN page ↗

Estimation of DIFferential COexpressed NETworks using diverse and user metrics. This package is basically used for three functions related to the estimation of differential coexpression. First, to estimate differential coexpression where the coexpression is estimated, by default, by Spearman correlation. For this, a metric to compare two correlation distributions is needed. The package includes 6 metrics. Some of them needs a threshold. A new metric can also be specified as a user function with specific parameters (see difconet.run). The significance is be estimated by permutations. Second, to generate datasets with controlled differential correlation data. This is done by either adding noise, or adding specific correlation structure. Third, to show the results of differential correlation analyses. Please see http://bioinformatica.mty.itesm.mx/difconet for further information.

Install

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

install.packages("difconet", 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-difconet

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-difconet

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-difconet

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

Health

CRAN checks

13OK

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

8

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

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 60%
Documented parameters: 65%
Return-value docs: 100%
References docs: 100%

Downloads

2.6K

CRAN downloads in the past year

Rank #17,488 · ~7/day · ~219/mo

Releases R versions

Daily download trend is not available in this view yet.

16530 days

63590 days

2.6K1 year

Compare downloads with other packages →

Also on103 r2u14 autocran

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.1.0gplots

Imports (7)

statsutilsstringr data.table mvtnormgraphicsgrDevices

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Victor Trevino

Author, Maintainer

Authors (2)

Victor Trevino

Author, Maintainer

Elpidio-Emmanuel Gonzalez-Valbuena

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0-4Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2017-05-31
Total releases: 1 / 9 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.1.0
Download size: 14 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("difconet")

Format

Trevino, V., & Gonzalez-Valbuena, E. (2017). difconet: Differential Coexpressed Networks (Version 1.0-4) [Computer software]. https://doi.org/10.32614/CRAN.package.difconet

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 difconet version 1.0-4 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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