readyomics

0.2.1

Ready-to-Use Omics Formatting, Analysis, and Visualization Pipeline

0packages depend

2.9Kdownloads / year

69.3%test coverage

13/13checks pass

Overview

About

Maintained by Laura Martinez-GiliFirst published 2025-08-205 releasesCRAN page ↗GitHub ↗

Provides a flexible and streamlined pipeline for formatting, analyzing, and visualizing omics data, regardless of omics type (e.g. transcriptomics, proteomics, metabolomics). The package includes tools for shaping input data into analysis-ready structures, fitting linear or mixed-effect models, extracting key contrasts, and generating a rich variety of ready-to-use publication-quality plots. Designed for transparency and reproducibility across a wide range of study designs, with customizable components for statistical modeling.

Install

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

install.packages("readyomics", 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("lmartinezgili/readyomics")

Development version from lmartinezgili/readyomics. 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-readyomics

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

# 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-readyomics

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

Health

CRAN checks

13OK

Slowest check: 5.4 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.65

69.3%

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
WARNING2026-06-07
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-11
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-10
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

OK2026-03-12
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 466 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 89%
Return-value docs: 100%
References docs: 20%

Downloads

2.9K

CRAN downloads in the past year

Rank #15,403 · ~8/day · ~238/mo

Releases R versions

Daily download trend is not available in this view yet.

30630 days

70990 days

2.9K1 year

Compare downloads with other packages →

Also on106 r2u36 autocran

Repository

GitHub ↗ lmartinezgili/readyomics

0Stars

0Forks

0Open issues

0Open PRs

5Releases

11Commits

1Contributors

11 commits · Last activity 2026-06-24

Releases over time

2025-08-15 · 12026-07-07 · 5

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/lmartinezgili/readyomics on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

28 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (15)

dplyr future future.apply ggplot2 lme4 lmerTestmethodspermute rlangstatsstringr tidyrutilsvegan zCompositions

LinkingTo (0)

none

Suggests (16)

ape data.table ggrepel ggridges IHW imputeLCMD knitr phyloseq progressr purrr qvalue reformulas rmarkdown ropls scales testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Laura Martinez-Gili

Maintainer, Author, Copyright holder

Authors (1)

Laura Martinez-Gili

Maintainer, Author, Copyright holder

Laura Martinez-Gili

Maintainer, Author, Copyright holder

Package Timeline

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

0.2.1Latest
2026-06-25 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.2.0
2025-10-20 · diff ↗
0.1.2
2025-09-18 · diff ↗
0.1.1
2025-08-27 · diff ↗
0.1.0
2025-08-20
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-08-20
Total releases: 5 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 234 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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