R Observatory: Metrics for OmicFlow version 1.6.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

OmicFlow

1.6.0

Fast and Efficient (Automated) Analysis of Sparse Omics Data

0packages depend

4.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Alem GusinacFirst published 2025-09-018 releasesCRAN page ↗GitHub ↗

A generalised data structure for fast and efficient loading and data munching of sparse omics data. The 'OmicFlow' requires an up-front validated metadata template from the user, which serves as a guide to connect all the pieces together by aligning them into a single object that is defined as an 'omics' class. Once this unified structure is established, users can perform manual subsetting, visualisation, and statistical analysis, or leverage the automated 'autoFlow' method to generate a comprehensive report.

Install

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

install.packages("OmicFlow", 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("agusinac/OmicFlow")

Development version from agusinac/OmicFlow. 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-omicflow

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: 5.3 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.45

not tracked

Coverage

100%

Documentation · exports

23

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 5 earlier snapshots

NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-16
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-13
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 96%
References docs: 33%

Downloads

4.2K

CRAN downloads in the past year

Rank #6,289 · ~11/day · ~347/mo

Releases R versions

Daily download trend is not available in this view yet.

31330 days

1.3K90 days

4.2K1 year

Compare downloads with other packages →

Also on175 r2u

Repository

GitHub ↗ agusinac/omicflow

4Stars

0Forks

4Open issues

0Open PRs

8Releases

298Commits

4Contributors

metagenomicsomicsproteomics

298 commits · Last activity 2026-08-12 · 0% stars, 30d

Stars over time

2026-01-29 · 12026-07-07 · 4

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/agusinac/omicflow on 2026-08-16.

Continuous integration (1)

GitHub Actions

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

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Depends (4)

R >= 4.3.0R6 data.tableMatrix

Imports (20)

ape ggpubr ggrepel ggplot2 jsonlite jsonvalidate magrittrmethodspatchwork RColorBrewer rhdf5 rstatix Rcpp RcppParallelstatstoolsutilsvegan yyjsonr cli

LinkingTo (3)

Rcpp RcppParallel RcppArmadillo

Suggests (4)

DT downloadthis rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Alem Gusinac

Author, Maintainer

Authors (3)

Alem Gusinac

Author, Maintainer

Annemarie Boleij

Author, Funder

Thomas Ederveen

Author

Funders (1)

Annemarie Boleij

Author, Funder

Package Timeline

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

1.6.0Latest
2026-05-19 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.5.1
2026-02-27 · diff ↗
1.5.0
2026-01-26 · diff ↗
1.4.2
2025-11-30 · diff ↗
1.4.0
2025-10-29 · diff ↗
1.3.2
2025-09-21 · diff ↗
1.3.1
2025-09-04 · diff ↗
1.3.0
2025-09-01
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-09-01
Total releases: 8 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.3.0
Download size: 187 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("OmicFlow")

Format

Gusinac, A., Boleij, A., & Ederveen, T. (2026). OmicFlow: Fast and Efficient (Automated) Analysis of Sparse Omics Data (Version 1.6.0) [Computer software]. https://doi.org/10.32614/CRAN.package.OmicFlow

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 OmicFlow version 1.6.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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