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.
Highlights
Recent advances from Oxford Nanopore Technologies (ONT) have enabled high-throughput, genome-wide long-read DNA methylation profiling using nanopore sequencers, without the need for bisulfite conversion [1, 2].A common goal of genome-wide profiling of DNA methylation is to discover differentially methylated regions (DMRs) between experimental groups
Developed nanopore sequencing technology enables DNA methylation measurement on long DNA molecules. This technology provides a new tool for investigating DNA methylation, a form of DNA modification that plays an essential role in early development, and is linked to some forms of cancer through adulthood
There is a lack of R/ Bioconductor software for effective visualization of methylation calls based on nanopore platforms, which hinders the analysis and presentation of results
Summary
Recent advances from Oxford Nanopore Technologies (ONT) have enabled high-throughput, genome-wide long-read DNA methylation profiling using nanopore sequencers, without the need for bisulfite conversion [1, 2].A common goal of genome-wide profiling of DNA methylation is to discover differentially methylated regions (DMRs) between experimental groups. We have developed NanoMethViz to create visualizations that give high resolution insights into the data to allow visual inspection of regions identified as differentially methylated by statistical methods. This software has been developed for compatibility with other software in the Bioconductor ecosystem [3], allowing for access to a wealth of existing statistical and genomic analysis methods. This provides compatibility with the comprehensive toolkit for representing and manipulating genomic regions provided by GenomicRanges [4], and the statistical methods for DMR analysis available in packages such as bsseq [5], DSS [6] and edgeR [7]
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