ArticleBioinformatics (Oxford, England)2021
Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Effects of a randomized controlled trial of unconditional cash transfers on epigenetic measures of ageing and cognition in children and mothers.Nature human behaviour · 2026Article
- Maternal Heat Shock Protein as a Potential Biomarker of Adaptation to Heat Stress during Pregnancy and Its Relation to Preterm Birth.Environmental science & technology · 2026Article
- Ultra-Processed Foods and the Cardiovascular-Kidney-Metabolic Continuum: Integrating Epidemiological, Multi-Omics, and Translational Evidence.Nutrients · 2026Review
- Covariate balanced allocation of samples to batches to mitigate the impacts of technical variability.Bioinformatics advances · 2026Article
- Genetic and environmental contributions to epigenetic aging across adolescence and young adulthood.Clinical epigenetics · 2025Article
- Tissue-specific methylomic responses to a lifestyle intervention in older adults associate with metabolic and physiological health improvements.Aging cell · 2025Article
- DNA methylation differences between cord and adult white blood cells reflect postnatal immune cell maturation.Communications biology · 2025Article
- A Comparison of Three Automated Nucleic Acid Extraction Systems for Human Stool Samples.Microorganisms · 2024Article
- DNA methylation patterns of FKBP5 regulatory regions in brain and blood of humanized mice and humans.Molecular psychiatry · 2024Article
- Proteomic Evolution from Acute to Post-COVID-19 Conditions.Journal of proteome research · 2024Article
- Injectiondesign: web service of plate design with optimized stratified block randomization for modern GC/LC-MS-based sample preparation.BMC bioinformatics · 2023Article
- Epigenetic age acceleration as a biomarker for impaired cognitive abilities in adulthood following early life adversity and psychiatric disorders.Neurobiology of stress · 2023Article
- Early-life exposure to cigarette smoke primes lung function and DNA methylation changes atAmerican journal of physiology. Lung cellular and molecular physiology · 2023Article
- Transdiagnostic evaluation of epigenetic age acceleration and burden of psychiatric disorders.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2023Article
- The Developing Human Connectome Project Neonatal Data Release.Frontiers in neuroscience · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
motivationBatch effects heavily impact results in omics studies, causing bias and false positive results, but software to control them preemptively is lacking. Sample randomization prior to measurement is vital for minimizing these effects, but current approaches are often ad hoc, poorly documented and ill-equipped to handle multiple batches and outcomes.
resultsWe developed Omixer-a Bioconductor package implementing multivariate and reproducible sample randomization for omics studies. It proactively counters correlations between technical factors and biological variables of interest by optimizing sample distribution across batches. AVAILABILITYAND IMPLEMENTATION: Omixer is available from Bioconductor at http://bioconductor.org/packages/release/bioc/html/Omixer.html. Scripts and data used to generate figures available upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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