R Observatory: Metrics for Patterns version 1.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Patterns

1.7

Deciphering Biological Networks with Patterned Heterogeneous Measurements

0packages depend

5.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Frederic BertrandFirst published 2019-06-078 releasesCRAN page ↗GitHub ↗

A modeling tool dedicated to biological network modeling (Bertrand and others 2020, doi:10.1093/bioinformatics/btaa855). It allows for single or joint modeling of, for instance, genes and proteins. It starts with the selection of the actors that will be the used in the reverse engineering upcoming step. An actor can be included in that selection based on its differential measurement (for instance gene expression or protein abundance) or on its time course profile. Wrappers for actors clustering functions and cluster analysis are provided. It also allows reverse engineering of biological networks taking into account the observed time course patterns of the actors. Many inference functions are provided and dedicated to get specific features for the inferred network such as sparsity, robust links, high confidence links or stable through resampling links. Some simulation and prediction tools are also available for cascade networks (Jung and others 2014, doi:10.1093/bioinformatics/btt705). Example of use with microarray or RNA-Seq data are provided.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("Patterns", 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("fbertran/Patterns")

Development version from fbertran/Patterns. 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-patterns

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

Health

CRAN checks

13OK

Slowest check: 5.7 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.03

not tracked

Coverage

100%

Documentation · exports

19

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

Documentation

READMEYes · 2,038 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 90%
Documented parameters: 100%
Return-value docs: 100%
References docs: 7%

Downloads

5.9K

CRAN downloads in the past year

Rank #7,350 · ~16/day · ~492/mo

Releases R versions

Daily download trend is not available in this view yet.

17930 days

1.2K90 days

5.9K1 year

Compare downloads with other packages →

Also on133 r2u19 c2d4u

Repository

GitHub ↗ fbertran/patterns

4Stars

0Forks

0Open issues

0Open PRs

5Releases

112Commits

4Contributors

112 commits · Last activity 2025-09-15

Stars over time

2019-08-15 · 32026-07-07 · 4

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/fbertran/patterns on 2026-08-09.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (19)

abindclustere1071 gplotsgraphicsgrDevicesigraph larslatticelimmamethodsMfuzz movMF nnls plotrix SelectBoost tnet VGAM WGCNA

LinkingTo (0)

none

Suggests (13)

animation Biobase biomaRt c060 CascadeData elasticnet glmnet knitr pixmap R.rsp rmarkdown spls testthat (>= 3.0.0)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Frederic Bertrand

Maintainer, Author

Authors (2)

Frederic Bertrand

Maintainer, Author

Myriam Maumy-Bertrand

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.7Latest
2025-09-15 · current release · diff ↗
1.6
2025-07-02 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.5
2024-05-06 · diff ↗
unarchivedReturned to CRAN
2024-05-06
archivedRemoved from CRAN
2024-05-04
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.4
2022-12-01 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.3
2021-03-21 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.2
2019-11-13 · diff ↗
1.1
2019-08-24 · diff ↗

Show 2 earlier events

1.0
2019-06-07
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-06-07
Total releases: 8 / 7 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 616 KB / 12 files
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Patterns")

Format

Bertrand, F., & Maumy-Bertrand, M. (2025). Patterns: Deciphering Biological Networks with Patterned Heterogeneous Measurements (Version 1.7) [Computer software]. https://doi.org/10.32614/CRAN.package.Patterns

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 Patterns version 1.7 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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