ArticlePLoS computational biology2021
NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Reactive oxygen species stimulate Paneth cell plasticity and diminish antimicrobial function.The EMBO journal · 2026Article
- Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End.Genome research · 2026Article
- Long-read sequencing reveals genomic and epigenomic variation in the dark genome of human Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma's information flow.Genome biology · 2025Article
- Rewriting nuclear epigenetic scripts in mitochondrial diseases as a strategy for heteroplasmy control.EMBO molecular medicine · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Methylmap: visualization of modified nucleotides for large cohort sizes.BMC bioinformatics · 2025Article
- Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology.Epigenetics & chromatin · 2024Review
- Sex differences in MAGEL2 gene promoter methylation in high functioning autism - trends from a pilot study using nanopore Cas9 targeted long read sequencing.BMC medical genomics · 2024Article
- Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing.Genome research · 2024Article
- Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges.International journal of molecular sciences · 2024Review
- A streamlined workflow for long-read DNA methylation analysis with NanoMethViz and Bioconductor.F1000Research · 2024Article
- A targeted long-read sequencing approach questions the association of OXTR methylation with high-functioning autism.Clinical epigenetics · 2023Article
- Increased paternal corticosterone exposure influences offspring behaviour and expression of urinary pheromones.BMC biology · 2023Article
- A tool for rapid, automated characterization of population epigenomics in plants.Scientific reports · 2023Article
- Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic Modifications.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Crossing Bacterial Genomic Features and Methylation Patterns with MeStudio: An Epigenomic Analysis Tool.International journal of molecular sciences · 2022Article
- Methylartist: tools for visualizing modified bases from nanopore sequence data.Bioinformatics (Oxford, England) · 2022Article
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A key benefit of long-read nanopore sequencing technology is the ability to detect modified DNA bases, such as 5-methylcytosine. The lack of R/Bioconductor tools for the effective visualization of nanopore methylation profiles between samples from different experimental groups led us to develop the NanoMethViz R package. Our software can handle methylation output generated from a range of different methylation callers and manages large datasets using a compressed data format. To fully explore the methylation patterns in a dataset, NanoMethViz allows plotting of data at various resolutions. At the sample-level, we use dimensionality reduction to look at the relationships between methylation profiles in an unsupervised way. We visualize methylation profiles of classes of features such as genes or CpG islands by scaling them to relative positions and aggregating their profiles. At the finest resolution, we visualize methylation patterns across individual reads along the genome using the spaghetti plot and heatmaps, allowing users to explore particular genes or genomic regions of interest. In summary, our software makes the handling of methylation signal more convenient, expands upon the visualization options for nanopore data and works seamlessly with existing methylation analysis tools available in the Bioconductor project. Our software is available at https://bioconductor.org/packages/NanoMethViz.
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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.