R Observatory: Metrics for Patterns version 1.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Patterns

1.7Package record

Deciphering Biological Networks with Patterned Heterogeneous Measurements

0packages depend

6.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Frederic BertrandCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.7

Updated maintainer email.
Added unit tests.
Added package doi.

From NEWS.md in the release

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. 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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.7 min · r-release-macos-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 1.7

READMEYes · 2,038 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.7Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 46 (1 internal)includes a package overview page
Examples that run: 88%37 run in a plain check · 5 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 7%

Vignettes (2)

How these are measured

Downloads

6.1K

CRAN downloads in the past year

Rank #7,165 · ~17/day · ~506/mo

Releases R versions

Daily download trend is not available in this view yet.

53730 days

1.2K90 days

6.1K1 year

Compare downloads with other packages →

Also on93 r2u39 c2d4u

How downloads are counted

Repository

fbertran/patterns ↗Account: fbertran

4Stars

0Forks

0Open issues

0Open PRs

5Releases

112Commits

4Commit identities

112 commits · Last activity 2025-09-15 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 1,799
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2019-08-15 · 32026-07-07 · 4

How these are measured

PracticesBeta

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

Checks run against github.com/fbertran/patterns on 2026-10-18.

Continuous integration (1)

GitHub Actions

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-09-15

pkgdown site last built 2025-09-15

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Installing Patterns adds 99 packages (56 with compiled code, 96 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 4 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Frederic Bertrand

Maintainer since 1.0 (2019), Author

Myriam Maumy-Bertrand

Author

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.7Latest
record
2025-09-15 · current release · diff ↗
1.6
record
2025-07-02 · diff ↗
R
R 4.5.0 released · 2025-04-11
unarchivedReturned to CRAN
2024-05-06
1.5
record
2024-05-06 · diff ↗
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
record
2022-12-01 · diff ↗ ·
removed 1 export
as.micro_array

added 1 export
as.omics_array
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.3
record
2021-03-21 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.2
record
2019-11-13 · diff ↗
1.1
record
2019-08-24 · diff ↗

Show 2 earlier eventsHide 2 earlier events

1.0
record
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

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")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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