ArticleBMC bioinformatics2018
Enhanced JBrowse plugins for epigenomics data visualization.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution.Nature plants · 2025Article
- SoyMD: a platform combining multi-omics data with various tools for soybean research and breeding.Nucleic acids research · 2024Article
- MethMarkerDB: a comprehensive cancer DNA methylation biomarker database.Nucleic acids research · 2024Article
- Enzymatic reactions of AGO4 in RNA-directed DNA methylation: siRNA duplex loading, passenger strand elimination, target RNA slicing, and sliced target retention.Genes & development · 2023Article
- Quality control and evaluation of plant epigenomics data.The Plant cell · 2022Article
- ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms.Nucleic acids research · 2022Article
- AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana.Nucleic acids research · 2021Article
- Anno genominis XX: 20 years of Arabidopsis genomics.The Plant cell · 2021Review
- Chromatin accessibility profiling methods.Nature reviews. Methods primers · 2021Article
- Araport Lives: An Updated Framework for Arabidopsis Bioinformatics.The Plant cell · 2020Article
- Using long-read sequencing to detect imprinted DNA methylation.Nucleic acids research · 2019Article
- Diversity of cytosine methylation across the fungal tree of life.Nature ecology & evolution · 2019Article
- dictyBase and the Dicty Stock Center (version 2.0) - a progress report.The International journal of developmental biology · 2019Review
- Genome sequences of horticultural plants: past, present, and future.Horticulture research · 2019Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundNew sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications.
resultsWe present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifically, we have focused on visualizing DNA base modifications, small non-coding RNAs, stranded read coverage, and sequence motif density. Additionally, we present several plugins for improved user experience such as configurable, high-quality screenshots.
conclusionsIn visualizing epigenomics with traditional genomics data, we see these plugins improving scientific communication and leading to discoveries within the field of epigenomics.
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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.