Welcome to MetaOmixTools

A modern suite for integrative meta-omics analysis combining gene ranking and functional enrichment.

Suite Description

MetaOmixTools is a bioinformatics suite designed for the integration and meta-analysis of omics data. The suite is composed of two main tools: MetaRank and MetaEnrich .

MetaRank specialises in the meta-analysis of pre-ranked (classified) gene lists. It accepts multiple studies (weighted or unweighted) and uses methods such as RankProd or RRA to generate a consensus gene ranking. Optionally, it performs an enrichment analysis of the top genes from the final consensus.

MetaEnrich performs a meta-analysis at the functional enrichment level. It takes one or multiple unranked gene lists, performs an overrepresentation analysis (ORA) on each of them, allowing the use of known databases such as GO, KEGG, Reactome, as well as custom annotations, and then combines the p-values (e.g., Fisher's method) to identify consensus functional terms enriched across all studies.

MetaRank Visual

MetaRank

MetaEnrich Visual

MetaEnrich





Excluded terms (below frequency threshold):








General overview of the MetaOmixTools suite.

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General overview of MetaRank module.

RankProd input panel.

Input interface for RRA analysis.

Information box for RankProd mode.

Information box for RRA mode.

RankProd parameter settings.

RRA parameter settings.

Group origin definition for RankProd.

Enrichment options after ranking.

Example data configuration (1).

Example data configuration (2).

Example data configuration (3).

Example data configuration (4).

Example data configuration (5).

Error example 1.

Error example 2.

Error example 3.

Error example 4.

Error example 5.

Error example 6.

Error example 7.

Error example 8.

Error example 9.

MetaRank full workflow.

UpSet plot of example dataset.

UpSet plot in Example 2.

Heatmap from Example 1.

Heatmap from Example 2.

Enrichment plot from Example 3.

Enrichment plot from Example 2.

General overview of MetaEnrich.

Input via file upload or text paste.

Contextual information menu (i).

Functional analysis parameters.

Combined results table.

Dotplot of enriched GO terms.

Barplot of enriched GO terms.

Workflow diagram of the analysis.

Input file format error.

Text paste input error.

Organism selection error.

Gene identifier error.

Error: no functional information available.

MetaOmixTools Suite & Individual Tools

Online Tools

You can launch each application individually:

GitHub Repositories

All apps are open-source and available on GitHub:

Suite Architecture

The suite is built using modular Shiny components. Each tool is encapsulated as a reusable module that can be independently loaded, improving maintainability, flexibility, and integration into larger workflows.

Web Tool Design Principles

The development of MetaOmixTools adheres to best practices in web-based scientific tools:

  • Reproducibility: All steps and computations are transparent and traceable.
  • Modularity: Tools are implemented as independent Shiny modules.
  • Clarity: The UI is designed to be minimalistic, responsive, and intuitive.
  • Accessibility: No installation required. Hosted online for direct usage.
  • Maintainability: Clear file structure and logical code separation for ease of updates.
  • Documentation: Every module and function is documented for both users and developers.
© Copyright 2026 , MetaOmixTools.
A modern suite for integrative meta-omics analysis combining gene ranking and functional enrichment.
Developed by The Centro de Investigación Príncipe Felipe (CIPF)
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