ArticleNAR genomics and bioinformatics2021
EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Stronger transgenerational plasticity in clonal compared to sexual offspring of Fragaria vesca: effects of drought, elevated temperature and CO2.Annals of botany · 2025Article
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- High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive transposable element superfamilies in the clonal Lombardy poplar.Journal of experimental botany · 2024Article
- Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca).BMC plant biology · 2024Article
- BSXplorer: analytical framework for exploratory analysis of BS-seq data.BMC bioinformatics · 2024Article
- DNA methylation correlates with transcriptional noise in response to elevated pCOEnvironmental epigenetics · 2024Article
- Herbivory induced methylation changes in the Lombardy poplar: A comparison of results obtained by epiGBS and WGBS.PloS one · 2023Article
- Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense.PLoS genetics · 2022Article
- Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches.BMC genomics · 2022Article
- DNA methylation dynamics during stress response in woodland strawberry (Horticulture research · 2022Article
- MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data.Quantitative plant biology · 2022Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The expanding scope and scale of next generation sequencing experiments in ecological plant epigenetics brings new challenges for computational analysis. Existing tools built for model data may not address the needs of users looking to apply these techniques to non-model species, particularly on a population or community level. Here we present a toolkit suitable for plant ecologists working with whole genome bisulfite sequencing; it includes pipelines for mapping, the calling of methylation values and differential methylation between groups, epigenome-wide association studies, and a novel implementation for both variant calling and discriminating between genetic and epigenetic variation.
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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.