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

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.

Version:	0.1.0
Depends:	R (≥ 4.1.0)
Imports:	dplyr, future, future.apply, ggplot2, lme4, lmerTest, methods, permute, rlang, stats, stringr, tidyr, utils, vegan, zCompositions
Suggests:	ape, data.table, ggrepel, ggridges, IHW, imputeLCMD, knitr, phyloseq, progressr, purrr, qvalue, rmarkdown, ropls, scales, testthat (≥ 3.0.0)
Published:	2025-08-20
DOI:	10.32614/CRAN.package.readyomics
Author:	Laura Martinez-Gili [cre, aut, cph]
Maintainer:	Laura Martinez-Gili <martinez.gili.laura at gmail.com>
BugReports:	https://github.com/lmartinezgili/readyomics/issues
License:	MIT + file LICENSE
URL:	https://lmartinezgili.github.io/readyomics/, https://github.com/lmartinezgili/readyomics
NeedsCompilation:	no
Materials:	README, NEWS
CRAN checks:	readyomics results

Documentation:

Reference manual:	readyomics.html , readyomics.pdf
Vignettes:	readyomics (source, R code)

Downloads:

Package source:	readyomics_0.1.0.tar.gz
Windows binaries:	r-devel: readyomics_0.1.0.zip, r-release: readyomics_0.1.0.zip, r-oldrel: readyomics_0.1.0.zip
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): readyomics_0.1.0.tgz

Linking:

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