ArticleBioinformatics (Oxford, England)2020
Methplotlib: analysis of modified nucleotides from nanopore sequencing.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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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
18 citing papers in PubMed, 38 citations in OpenAlex.
- Computational analysis of DNA methylation from long-read sequencing.Nature reviews. Genetics · 2025Review
- Methylmap: visualization of modified nucleotides for large cohort sizes.BMC bioinformatics · 2025Article
- Nanopore Long-Read Sequencing as a First-Tier Diagnostic Test to Detect Repeat Expansions in Neurological Disorders.International journal of molecular sciences · 2025Article
- Mapping protein-DNA interactions with DiMeLo-seq.Nature protocols · 2024Article
- Figeno: multi-region genomic figures with long-read support.Bioinformatics (Oxford, England) · 2024Article
- Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges.International journal of molecular sciences · 2024Review
- Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae.BMC genomics · 2024Article
- CGG repeat expansion in LRP12 in amyotrophic lateral sclerosis.American journal of human genetics · 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
- High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads.Genomics, proteomics & bioinformatics · 2022Article
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
- Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing.Nature biotechnology · 2021Article
- NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data.PLoS computational biology · 2021Article
- DNAModAnnot: a R toolbox for DNA modification filtering and annotation.Bioinformatics (Oxford, England) · 2021Article
- Cas9-targeted nanopore sequencing reveals epigenetic heterogeneity afterMicrobial genomics · 2021Article
- Rapid Characterization of Complex Killer Cell Immunoglobulin-Like Receptor (KIR) Regions Using Cas9 Enrichment and Nanopore Sequencing.Frontiers in immunology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryModified nucleotides play a crucial role in gene expression regulation. Here, we describe methplotlib, a tool developed for the visualization of modified nucleotides detected from Oxford Nanopore Technologies sequencing platforms, together with additional scripts for statistical analysis of allele-specific modification within-subjects and differential modification frequency across subjects. AVAILABILITY AND IMPLEMENTATION: The methplotlib command-line tool is written in Python3, is compatible with Linux, Mac OS and the MS Windows 10 Subsystem for Linux and released under the MIT license. The source code can be found at https://github.com/wdecoster/methplotlib and can be installed from PyPI and bioconda. Our repository includes test data, and the tool is continuously tested at travis-ci.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.