OSCR

MetaOmixTools: A User-Friendly Web Suite for Meta-analysis of Ranked Features and Functional Enrichment.

Code ↔ Paper

5 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 5 matches
  1. [1] § Methods › MetaEnrich module ↔ modules/metaenrichgo/mod_metaenrichgo.R, lines 182–222 · score 0.83 · Mus musculus, Rattus norvegicus, Homo sapiens, Tippett, Wilkinson, Stouffer
  2. [2] § Methods › MetaEnrich module ↔ metaenrichgo_readme.qmd, lines 12–121 · score 0.80 · Mus musculus, Rattus norvegicus, Kyoto Encyclopedia, Homo sapiens, Gene Ontology, Genomes
  3. [3] § Methods › MetaRank module ↔ metarank_readme.qmd, lines 603–678 · score 0.69 · RobustRankAggreg, RankProd, pre ranked, top ranked, proteins, consensus ranking
  4. [4] § Methods ↔ metarank_readme.qmd, lines 603–678 · score 0.62 · Kyoto Encyclopedia, Gene Ontology, pre ranked, robust rank, top ranked, meta ranking
  5. [5] § Methods › MetaRank module ↔ metarank_example.qmd, lines 651–713 · score 0.58 · RobustRankAggreg, top ranked, proteins, consensus ranking, probabilistic, geometric

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Quarto · 1,189 lines · 84 KB · no license · 2 matches

The registry keeps no copy of this file: its repository has no license, so its authors keep all their rights to it. Your browser shows it from its source, with JavaScript.

It can be read at the source: metarank_readme.qmd.

Overview

Authors: Rubén Grillo-Risco1, Maksym Kupchyk Tiurin2, Carla Perpiñá-Clérigues1, Francisco J. Cordero Felipe3, Samuel Lozano Juárez4,5, María Iglesia-Vayá6, Francisco García-García1
ORCID iDs: Rubén Grillo-Risco, Maksym Kupchyk Tiurin, Carla Perpiñá-Clérigues, Francisco J. Cordero Felipe, Samuel Lozano Juárez, María Iglesia-Vayá, Francisco García-García
  1. Computational Biomedicine Laboratory, Principe Felipe Research Centre (CIPF), Valencia 46012, Spain
  2. Molecular, Cellular and Genomic Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
  3. Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
  4. Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
  5. Escuela de Doctorado, Universidad Autónoma de Madrid, Madrid, Spain
  6. Joint Unit in Biomedical Imaging and Artificial Intelligence FISABIO-CIPF, Foundation for the Promotion of Health and Biomedical Research of Valencia Region, Valencia, Spain
Institutions: Centro de Investigacion Principe Felipe (Spain); Instituto de Investigación Sanitaria La Fe (Spain); Instituto de Biomedicina de Valencia (Spain); Spanish National Centre for Cardiovascular Research (Spain); Universidad Autónoma de Madrid (Spain); Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (Spain)
Journal: Computational and structural biotechnology journal, volume 35, issue 1, article 0157
Dates: received 9 April 2026; accepted 13 June 2026; published online 30 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.34133/csbj.0157 · PMID 42614712 · PMCID PMC13483920 · OpenAlex W7164734023
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: other condition (population)
Methods: Statistics, Preprocessing
Journal subjects: Software/Web Server Article
Topic: Meta-analysis and systematic reviews (Statistics, Probability and Uncertainty, Decision Sciences), according to OpenAlex
Funding: Conselleria de Cultura, Educación y Ciencia, Generalitat Valenciana (CIAICO/2023/149); Conselleria d’Educació, Investigació, Cultura i Esport (CIGE/2024/242); Ministerio de Ciencia e Innovación (PID2021-124430OA-I00)
Citations: not cited yet (Europe PMC); 49 references in the paper

Abstract

The growing number of omics datasets in public repositories provides an opportunity to enhance data reusability through data integration; however, complex statistical barriers often hinder the effective combination of independent studies. To address this problem, we present MetaOmixTools, an interactive web-based suite that streamlines the meta-analysis of ranked feature lists and functional enrichment profiles. The platform integrates 2 primary modules—MetaRank and MetaEnrich—within a code-free environment. MetaRank generates robust consensus rankings from multiple lists by implementing weighted (e.g., rank product) and unweighted (e.g., robust rank aggregation) strategies, while MetaEnrich performs functional meta-analyses by combining probability values from individual overrepresentation analyses using established statistical techniques. Using case studies, we established consensus rankings for acute spinal cord injury across heterogeneous platforms, identifying conserved inflammatory marker genes in the up-regulated gene list (e.g., Slpi, Ccl2, and Msr1) and synaptic loss genes in the down-regulated gene list (e.g., Kcna2, Dao, and Ppp1r1b), and also characterized inverse functional intersections between melanoma brain metastasis and neurodegenerative diseases. By providing intuitive, real-time visualization and reproducible workflows, MetaOmixTools empowers the research community to extract consistent biological insights from multistudy data. We have made MetaOmixTools freely available at https://bioinfo.cipf.es/metaomixtools/.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 5 matches between paragraphs and lines of code.

emekate00/metaomixtools

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 2716e997b8f6a909ae19a15d2da9f2e6da2dea52, 20 February 2026
Languages: JavaScript (52), R (11), Quarto (7)
Size: 517 files, 70 scripts
Software Heritage: not archived
Found in: “Data Availability”
Holds: 7 notebooks
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (4 files), Plotly (4 files), tidyverse (4 files), clusterProfiler (3 files), data.table (2 files)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
70 files, not copied: shown from their source

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At the source: github.com/emekate00/metaomixtools

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 70 scripts, each with its path and the digest of its content;
  • 5 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data Availability

The code is available at https://github.com/emekate00/metaomixtools. The web tool is openly available at https://bioinfo.cipf.es/metaomixtools/.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 3 funders, 41 references.

Cite

This paper

Grillo-Risco, R., Tiurin, M. K., Perpiñá-Clérigues, C., Cordero Felipe, F. J., Juárez, S. L., Iglesia-Vayá, M., & García-García, F. (2026). MetaOmixTools: A User-Friendly Web Suite for Meta-analysis of Ranked Features and Functional Enrichment. Computational and structural biotechnology journal, 35(1), 0157. https://doi.org/10.34133/csbj.0157

BibTeX

@article{grillorisco2026metaomixtools,
author = {Grillo-Risco, Rubén and Tiurin, Maksym Kupchyk and Perpiñá-Clérigues, Carla and Cordero Felipe, Francisco J. and Juárez, Samuel Lozano and Iglesia-Vayá, María and García-García, Francisco},
title = {{MetaOmixTools: A User-Friendly Web Suite for Meta-analysis of Ranked Features and Functional Enrichment}},
journal = {Computational and structural biotechnology journal},
year = {2026},
month = jun,
volume = {35},
number = {1},
pages = {0157},
publisher = {AAAS Science Partner Journal Program},
issn = {2001-0370},
doi = {10.34133/csbj.0157},
url = {https://doi.org/10.34133/csbj.0157},
pmid = {42614712},
pmcid = {PMC13483920}
}

RIS

TY - JOUR
AU - Grillo-Risco, Rubén
AU - Tiurin, Maksym Kupchyk
AU - Perpiñá-Clérigues, Carla
AU - Cordero Felipe, Francisco J.
AU - Juárez, Samuel Lozano
AU - Iglesia-Vayá, María
AU - García-García, Francisco
TI - MetaOmixTools: A User-Friendly Web Suite for Meta-analysis of Ranked Features and Functional Enrichment
T2 - Computational and structural biotechnology journal
J2 - Comput Struct Biotechnol J
PY - 2026
DA - 2026/06/30
VL - 35
IS - 1
SP - 0157
SN - 2001-0370
PB - AAAS Science Partner Journal Program
DO - 10.34133/csbj.0157
UR - https://doi.org/10.34133/csbj.0157
LA - en
ER -

CSL-JSON

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The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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