NanoMethViz

DOI: 10.18129/B9.bioc.NanoMethViz  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see NanoMethViz.

Visualise methlation data from Oxford Nanopore sequencing

Bioconductor version: 3.16

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>

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")

 

HTML	R Script	Dimensionality Reduction
HTML	R Script	Exon Annotations
HTML	R Script	Importing/Exporting Data
HTML	R Script	Introduction
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialMethylation, Software, Visualization
Version	2.4.2
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 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, ggrastr, glue, graphics, limma(>= 3.44.0), patchwork, purrr, rlang, R.utils, RSQLite, Rsamtools, scales (>= 1.2.0), scico, stats, stringr, tibble, tidyr, utils, withr, zlibbioc
LinkingTo	Rcpp
Suggests	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, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr
SystemRequirements	C++11
Enhances
URL	https://github.com/shians/NanoMethViz
BugReports	https://github.com/Shians/NanoMethViz/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	NanoMethViz_2.4.2.tar.gz
Windows Binary	NanoMethViz_2.4.2.zip
macOS Binary (x86_64)	NanoMethViz_2.4.2.tgz
macOS Binary (arm64)	NanoMethViz_2.4.2.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