ArticleGenome biology2019
RnBeads 2.0: comprehensive analysis of DNA methylation data.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 220 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
220 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Epigenome-wide meta-analysis identifies DNA methylation biomarkers associated with diabetic kidney disease.Nature communications · 2022Pooled it
- Pooled it
- A predictive endocrine resistance index accurately stratifies luminal breast cancer treatment responders and nonresponders.The Journal of clinical investigation · 2025Trial
- Effects of Mediterranean diet during pregnancy on the onset of overweight or obesity in the offspring: a randomized trial.International journal of obesity (2005) · 2025Trial
- Epigenetic Insights in Pediatric Multiple Sclerosis: DNA Methylation Highlights an Involvement of Epstein-Barr Virus Infection and Host Immune Networks.Neurology(R) neuroimmunology & neuroinflammation · 2026Article
- Recurrent mechanisms of biallelic epigenetic inactivation reveal new putative tumour suppressor genes in prostate cancer.Nature communications · 2026Article
- DiffMethylTools: a toolbox for the detection, annotation, and visualization of differential methylation.Life science alliance · 2026Article
- Age-associated epigenomic heterogeneity in papillary tumors of the pineal region: a multicenter YoungNOA investigation.Acta neuropathologica communications · 2026Article
- Genome-wide DNA methylation analysis revealed epigenetic mechanism underlying end-stage renal disease.Nature communications · 2026Article
- Genome-Wide Assessment of DNA Methylation Fidelity Identifies Representative Ovarian Cancer Cell Line Models.Journal of cellular and molecular medicine · 2026Article
- Methylation profiling and alternative classification approaches in a glioma-enriched FFPE stereotaxic biopsy cohort.Acta neuropathologica communications · 2026Article
- Epigenome-Wide DNA Methylation Levels During Pregnancy: Associations with Parity Across Diverse Populations.Epigenomes · 2026Article
- CpGene: a web application for epigenetic signature identification from DNA methylation arrays.Bioinformatics (Oxford, England) · 2026Article
- Peripheral blood DNA methylation profile and immune checkpoint inhibitor response in cancer patients.ESMO open · 2026Article
- Tumor DNA methylation subtypes predict immunotherapy outcomes in pleural mesothelioma patients in the NIBIT-EPI-MESO study.Nature genetics · 2026Article
- Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets.Molecular systems biology · 2026Article
- GLYATL1 is associated with metabolic and epigenetic changes and with endocrine resistance in luminal breast cancer.Clinical epigenetics · 2026Article
- Epigenetic Instability-Based Metrics in Cell-Free DNA for Early Cancer Detection.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Longitudinal study of genome-wide DNA methylation in individuals with and without post-acute symptoms following SARS-CoV-2 infection.Epigenomics · 2026Article
- Complementary multi-omics profiling of chronic thromboembolic pulmonary hypertension reveals immune cell alterations, epigenetic changes, and genetically supported candidate genes.Animal models and experimental medicine · 2026Article
160 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
DNA methylation is a widely investigated epigenetic mark with important roles in development and disease. High-throughput assays enable genome-scale DNA methylation analysis in large numbers of samples. Here, we describe a new version of our RnBeads software - an R/Bioconductor package that implements start-to-finish analysis workflows for Infinium microarrays and various types of bisulfite sequencing. RnBeads 2.0 ( https://rnbeads.org/ ) provides additional data types and analysis methods, new functionality for interpreting DNA methylation differences, improved usability with a novel graphical user interface, and better use of computational resources. We demonstrate RnBeads 2.0 in four re-runnable use cases focusing on cell differentiation and cancer.
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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.