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NanoMethViz

Visualise methylation data from Oxford Nanopore sequencing

Bioconductor version: 3.23 · Package version: 3.8.0

NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("NanoMethViz")

Details

MaintainerShian Su <su.s@wehi.edu.au>
AuthorShian Su [cre, aut]
LicenseApache License (>= 2.0)
URLhttps://github.com/shians/NanoMethViz, https://shians.github.io/NanoMethViz/
Bug Reportshttps://github.com/Shians/NanoMethViz/issues
System RequirementsC++20
Downloads rank339
Source branchRELEASE_3_23
biocViewsDNAMethylation, DataImport, DifferentialMethylation, Epigenetics, LongRead, Software, Visualization

Documentation

Download

Dependencies

Depends: R (>= 4.0.0), methods, ggplot2 (>= 3.4.0)

Imports: cpp11 (>= 0.2.5), readr, cli, S4Vectors, SummarizedExperiment, BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, dbscan, e1071, fs, GenomicRanges, Biostrings, ggrastr, glue, graphics, IRanges, limma (>= 3.44.0), patchwork, purrr, rlang, R.utils, Rsamtools, scales (>= 1.2.0), stats, stringr, tibble, tidyr, utils, withr

LinkingTo: Rcpp

Suggests: BiocStyle, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr