OmicNavigator

1.19.0

Open-Source Software for 'Omic' Data Analysis and Visualization

0packages depend

4.1Kdownloads / year

92.4%test coverage

13/13checks pass

Overview

About

Maintained by Brett EngelmannFirst published 2021-07-269 releasesCRAN page ↗GitHub ↗

A tool for interactive exploration of the results from 'omics' experiments to facilitate novel discoveries from high-throughput biology. The software includes R functions for the 'bioinformatician' to deposit study metadata and the outputs from statistical analyses (e.g. differential expression, enrichment). These results are then exported to an interactive JavaScript dashboard that can be interrogated on the user's local machine or deployed online to be explored by collaborators. The dashboard includes 'sortable' tables, interactive plots including network visualization, and fine-grained filtering based on statistical significance.

Install

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

install.packages("OmicNavigator", 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("abbvie-external/OmicNavigator")

Development version from abbvie-external/OmicNavigator. 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-omicnavigator

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-OmicNavigator

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-OmicNavigator

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

Health

CRAN checks

13OK

Slowest check: 6.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.00

92.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

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 · 1,085 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 97%
References docs: 11%

Downloads

4.1K

CRAN downloads in the past year

Rank #12,636 · ~11/day · ~341/mo

Releases R versions

Daily download trend is not available in this view yet.

28130 days

81790 days

4.1K1 year

Compare downloads with other packages →

Also on126 r2u20 autocran1.8K conda_forge27 c2d4u

Repository

GitHub ↗ abbvie-external/omicnavigator

42Stars

13Forks

0Open issues

2Open PRs

91Releases

957Commits

70Contributors

bioinformaticsgenomicsomicsopencpur

957 commits · Last activity 2026-02-25 · 0% stars, 30d

Stars over time

2025-05-28 · 352026-07-07 · 42

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/abbvie-external/omicnavigator on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

MakefileDockerfile

Lint, format, editor (1)

RStudio project

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.2.0

Imports (6)

data.tablegraphicsjsonlitestatstoolsutils

LinkingTo (0)

none

Suggests (7)

faviconPlease ggplot2 opencpu plotly tinytest ttdo UpSetR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (11)

Maintainer (1)

Brett Engelmann

Author, Maintainer

Authors (9)

Author, Maintainer

Author

Author

Author · added in 1.8.0

Joe Dalen

Author

Terrence Ernst

Author

Joe LoGrasso

Author · added in 1.11.5

Justin Moore

Author

Paul Nordlund

Author

Contributors (1)

Elyse Geoffroy

Contributor · added in 1.15.0

AbbVie Inc.

Funders (1)

AbbVie Inc.

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.19.0Latest
2025-12-17 · current release · diff ↗
1.16.0
2025-07-30 · diff ↗
1.15.0
2025-05-28 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.13.13
2023-08-25 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.13.6
2023-01-12 · diff ↗
1.11.5
2022-05-26 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.8.0
2021-12-01 · diff ↗
1.4.3
2021-08-05 · diff ↗
1.4.2
2021-07-26
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-26
Total releases: 9 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.2.0
Bundled data: 4.6 KB / 1 file
Download size: 690 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Report a problem with this page →