ArticleGenome biology2023
pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- diffMONT: predicting methylation-specific PCR biomarkers based on nanopore sequencing data for clinical application.Bioinformatics (Oxford, England) · 2026Article
- Evaluation of Illumina and Oxford Nanopore Sequencing for the Study of DNA Methylation in Alzheimer's Disease and Frontotemporal Dementia.International journal of molecular sciences · 2025Review
- Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications.World journal of microbiology & biotechnology · 2025Review
- MethylomeMiner: A novel tool for high-resolution analysis of bacterial methylation patterns from nanopore sequencing.Computational and structural biotechnology journal · 2025Article
- Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP.Journal of industrial microbiology & biotechnology · 2024Article
- Stress-induced epigenetic effects driven by maternal lactation in dairy cattle: a comethylation network approach.Epigenetics · 2024Article
- A streamlined workflow for long-read DNA methylation analysis with NanoMethViz and Bioconductor.F1000Research · 2024Article
- Nanopore sequencing reveals methylation changes associated with obesity in circulating cell-free DNA from Göttingen Minipigs.Epigenetics · 2023Article
- Article
- A tool for rapid, automated characterization of population epigenomics in plants.Scientific reports · 2023Article
- Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures.Cell genomics · 2023Article
- From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research.Life (Basel, Switzerland) · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present pycoMeth, a toolbox to store, manage and analyze DNA methylation calls from long-read sequencing data obtained using the Oxford Nanopore Technologies sequencing platform. Building on a novel, rapid-access, read-level and reference-anchored methylation storage format MetH5, we propose efficient algorithms for haplotype aware, multi-sample consensus segmentation and differential methylation testing. We show that MetH5 is more efficient than existing solutions for storing Oxford Nanopore Technologies methylation calls, and carry out benchmarking for pycoMeth segmentation and differential methylation testing, demonstrating increased performance and sensitivity compared to existing solutions designed for short-read methylation data.
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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 Socratic graph.