NanoMethViz

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see NanoMethViz.

Visualise methlation data from Oxford Nanopore sequencing

Bioconductor version: 3.15

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.

Author: Shian Su [cre, aut]

Maintainer: Shian Su <su.s at wehi.edu.au>

Citation (from within R, enter citation("NanoMethViz")):

Installation

To install this package, start R (version "4.2") and enter:


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

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("NanoMethViz")

Dimensionality Reduction HTML R Script

Exon Annotations HTML R Script

Importing/Exporting Data HTML R Script

Introduction HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialMethylation, Software, Visualization

Version 2.2.0

In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)

License Apache License (>= 2.0)

Depends R (>= 4.0.0), methods, ggplot2

Imports cpp11 (>= 0.2.5), readr, S4Vectors, SummarizedExperiment, BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, data.table, e1071, fs, GenomicRanges, glue, limma(>= 3.44.0), patchwork, purrr, rlang, RSQLite, Rsamtools, scales, scico, stats, stringr, tibble, tidyr, utils, withr, zlibbioc

System Requirements C++11

URL https://github.com/shians/NanoMethViz

Bug Reports https://github.com/Shians/NanoMethViz/issues

Suggests DSS, Mus.musculus, Homo.sapiens, knitr, rmarkdown, testthat (>= 3.0.0), covr

Linking To Rcpp

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