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BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization

The amount of biological data, generated with (single cell) omics technologies, is rapidly increasing, thereby exacerbating bottlenecks in the data analysis and interpretation of omics experiments. Data mining platforms that facilitate non-bioinformatician experimental scientists to analyze a wide r...

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Autores principales: Taverna, Federico, Goveia, Jermaine, Karakach, Tobias K, Khan, Shawez, Rohlenova, Katerina, Treps, Lucas, Subramanian, Abhishek, Schoonjans, Luc, Dewerchin, Mieke, Eelen, Guy, Carmeliet, Peter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319461/
https://www.ncbi.nlm.nih.gov/pubmed/32392297
http://dx.doi.org/10.1093/nar/gkaa332
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author Taverna, Federico
Goveia, Jermaine
Karakach, Tobias K
Khan, Shawez
Rohlenova, Katerina
Treps, Lucas
Subramanian, Abhishek
Schoonjans, Luc
Dewerchin, Mieke
Eelen, Guy
Carmeliet, Peter
author_facet Taverna, Federico
Goveia, Jermaine
Karakach, Tobias K
Khan, Shawez
Rohlenova, Katerina
Treps, Lucas
Subramanian, Abhishek
Schoonjans, Luc
Dewerchin, Mieke
Eelen, Guy
Carmeliet, Peter
author_sort Taverna, Federico
collection PubMed
description The amount of biological data, generated with (single cell) omics technologies, is rapidly increasing, thereby exacerbating bottlenecks in the data analysis and interpretation of omics experiments. Data mining platforms that facilitate non-bioinformatician experimental scientists to analyze a wide range of experimental designs and data types can alleviate such bottlenecks, aiding in the exploration of (newly generated or publicly available) omics datasets. Here, we present BIOMEX, a browser-based software, designed to facilitate the Biological Interpretation Of Multi-omics EXperiments by bench scientists. BIOMEX integrates state-of-the-art statistical tools and field-tested algorithms into a flexible but well-defined workflow that accommodates metabolomics, transcriptomics, proteomics, mass cytometry and single cell data from different platforms and organisms. The BIOMEX workflow is accompanied by a manual and video tutorials that provide the necessary background to navigate the interface and get acquainted with the employed methods. BIOMEX guides the user through omics-tailored analyses, such as data pretreatment and normalization, dimensionality reduction, differential and enrichment analysis, pathway mapping, clustering, marker analysis, trajectory inference, meta-analysis and others. BIOMEX is fully interactive, allowing users to easily change parameters and generate customized plots exportable as high-quality publication-ready figures. BIOMEX is open source and freely available at https://www.vibcancer.be/software-tools/biomex.
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spelling pubmed-73194612020-07-01 BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization Taverna, Federico Goveia, Jermaine Karakach, Tobias K Khan, Shawez Rohlenova, Katerina Treps, Lucas Subramanian, Abhishek Schoonjans, Luc Dewerchin, Mieke Eelen, Guy Carmeliet, Peter Nucleic Acids Res Web Server Issue The amount of biological data, generated with (single cell) omics technologies, is rapidly increasing, thereby exacerbating bottlenecks in the data analysis and interpretation of omics experiments. Data mining platforms that facilitate non-bioinformatician experimental scientists to analyze a wide range of experimental designs and data types can alleviate such bottlenecks, aiding in the exploration of (newly generated or publicly available) omics datasets. Here, we present BIOMEX, a browser-based software, designed to facilitate the Biological Interpretation Of Multi-omics EXperiments by bench scientists. BIOMEX integrates state-of-the-art statistical tools and field-tested algorithms into a flexible but well-defined workflow that accommodates metabolomics, transcriptomics, proteomics, mass cytometry and single cell data from different platforms and organisms. The BIOMEX workflow is accompanied by a manual and video tutorials that provide the necessary background to navigate the interface and get acquainted with the employed methods. BIOMEX guides the user through omics-tailored analyses, such as data pretreatment and normalization, dimensionality reduction, differential and enrichment analysis, pathway mapping, clustering, marker analysis, trajectory inference, meta-analysis and others. BIOMEX is fully interactive, allowing users to easily change parameters and generate customized plots exportable as high-quality publication-ready figures. BIOMEX is open source and freely available at https://www.vibcancer.be/software-tools/biomex. Oxford University Press 2020-07-02 2020-05-11 /pmc/articles/PMC7319461/ /pubmed/32392297 http://dx.doi.org/10.1093/nar/gkaa332 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server Issue
Taverna, Federico
Goveia, Jermaine
Karakach, Tobias K
Khan, Shawez
Rohlenova, Katerina
Treps, Lucas
Subramanian, Abhishek
Schoonjans, Luc
Dewerchin, Mieke
Eelen, Guy
Carmeliet, Peter
BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization
title BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization
title_full BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization
title_fullStr BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization
title_full_unstemmed BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization
title_short BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization
title_sort biomex: an interactive workflow for (single cell) omics data interpretation and visualization
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319461/
https://www.ncbi.nlm.nih.gov/pubmed/32392297
http://dx.doi.org/10.1093/nar/gkaa332
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