ArticleBMC bioinformatics2018
Integrating omics datasets with the OmicsPLS package.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
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- Multi-omics reveal molecular changes during suspension adaptation of HEK293 cells.Applied microbiology and biotechnology · 2026Article
- Multi-omics profiling of the diabetic human heart reveals coupled dysregulation in lipid metabolism, mitophagy, and extracellular matrix remodeling.Genome medicine · 2026Article
- An Integrative Proteotranscriptomics Approach Reveals New ADAM9 Substrates and Downstream Pathways.Molecular & cellular proteomics : MCP · 2026Article
- moiraine: an R package to construct reproducible pipelines for the application and comparison of multi-omics integration methods.Bioinformatics (Oxford, England) · 2026Article
- Integrated multi-omics analysis reveals candidate genes for cuticular wax biosynthesis and molecular characteristics of a glossy mutant in rapeseed under natural drought stress.Frontiers in plant science · 2026Article
- Restaurant occupational exposure affects the profiles of oral and gut pathobiomes and resistomes.Frontiers in microbiology · 2026Article
- Multi-Omics Analyses Reveal the Antifungal Mechanism of Phenazine-1-Carboxylic Acid AgainstJournal of fungi (Basel, Switzerland) · 2025Article
- Statistical modelling of an outcome variable with integrated multi-omics.BMC bioinformatics · 2025Article
- Integrated multi-omics identifies plant hormone signal transduction and phenylpropanoid biosynthesis as key pathways in kiwifruit (Actinidia chinensis var. deliciosa) resistance to Botryosphaeria Dothidea infection.BMC plant biology · 2025Article
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- Gut microbiome and plasma metabolome alterations in ileostomy and after closure of ileostomy.Microbiology spectrum · 2025Article
- Multi-Omics Profiling of Lipid Variation and Regulatory Mechanisms in Poultry Breast Muscles.Animals : an open access journal from MDPI · 2025Article
- Integrated metabolomic and transcriptomic analysis of anthocyanin metabolism in wheat pericarp.BMC genomic data · 2025Article
- Artificial intelligence: the human response to approach the complexity of big data in biology.GigaScience · 2025Review
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- Multi-omics decodes host-specific and environmental microbiome interactions in sepsis.Frontiers in microbiology · 2025Review
- The Impact of Nutrient Solution Electrical Conductivity on Leaf Transcriptome Contributing to the Fruit Quality of Cucumber Grown in Coir Cultivation.International journal of molecular sciences · 2024Article
- Metabolite profiling and transcriptome analyses reveal defense regulatory network against pink tea mite invasion in tea plant.BMC genomics · 2024Article
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Authors and funding
7 authors.
Funding
Abstract
backgroundWith the exponential growth in available biomedical data, there is a need for data integration methods that can extract information about relationships between the data sets. However, these data sets might have very different characteristics. For interpretable results, data-specific variation needs to be quantified. For this task, Two-way Orthogonal Partial Least Squares (O2PLS) has been proposed. To facilitate application and development of the methodology, free and open-source software is required. However, this is not the case with O2PLS.
resultsWe introduce OmicsPLS, an open-source implementation of the O2PLS method in R. It can handle both low- and high-dimensional datasets efficiently. Generic methods for inspecting and visualizing results are implemented. Both a standard and faster alternative cross-validation methods are available to determine the number of components. A simulation study shows good performance of OmicsPLS compared to alternatives, in terms of accuracy and CPU runtime. We demonstrate OmicsPLS by integrating genetic and glycomic data.
conclusionsWe propose the OmicsPLS R package: a free and open-source implementation of O2PLS for statistical data integration. OmicsPLS is available at https://cran.r-project.org/package=OmicsPLS and can be installed in R via install.packages("OmicsPLS").
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.