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NanoMethViz

This is the development version of NanoMethViz; for the stable release version, see NanoMethViz.

Visualise methylation data from Oxford Nanopore sequencing


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
User's Guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, LongRead, Software, Visualization
Version 2.99.8
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Apache License (>= 2.0)
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, data.table, dbscan, e1071, fs, GenomicRanges, Biostrings, ggrastr, glue, graphics, IRanges, limma(>= 3.44.0), patchwork, purrr, rlang, R.utils, Rsamtools, scales (>= 1.2.0), scico, stats, stringr, tibble, tidyr, utils, withr, zlibbioc
System Requirements C++20
URL https://github.com/shians/NanoMethViz
Bug Reports https://github.com/Shians/NanoMethViz/issues
See More
Suggests BiocStyle, DSS, 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
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package NanoMethViz_2.99.8.tar.gz
Windows Binary NanoMethViz_2.99.8.zip
macOS Binary (x86_64) NanoMethViz_2.99.8.tgz
macOS Binary (arm64) NanoMethViz_2.99.8.tgz
Source Repository git clone https://git.bioconductor.org/packages/NanoMethViz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NanoMethViz
Bioc Package Browser https://code.bioconductor.org/browse/NanoMethViz/
Package Short Url https://bioconductor.org/packages/NanoMethViz/
Package Downloads Report Download Stats