NanoMethViz

Visualise methlation data from Oxford Nanopore sequencing

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews	DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, Software, Visualization
Version	2.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	Apache License (>= 2.0)
Depends	R (>= 4.0.0), methods, ggplot2 (>= 3.4.0)
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
Linking To	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
System Requirements	C++20
Enhances
URL	https://github.com/shians/NanoMethViz
Bug Reports	https://github.com/Shians/NanoMethViz/issues

Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	NanoMethViz_2.6.0.tar.gz
Windows Binary	NanoMethViz_2.6.0.zip (64-bit only)
macOS Binary (x86_64)	NanoMethViz_2.6.0.tgz
macOS Binary (arm64)	NanoMethViz_2.6.0.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