NanoMethViz

DOI: 10.18129/B9.bioc.NanoMethViz    

Visualise methlation data from Oxford Nanopore sequencing

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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 Importing Data
HTML R Script Introduction
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialMethylation, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License Apache License (>= 2.0)
Depends R (>= 4.0.0), methods, ggplot2
Imports S4Vectors, SummarizedExperiment, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, data.table, e1071, fs, GenomicRanges, ggthemes, glue, patchwork, purrr, readr, rlang, RSQLite, Rsamtools, scales, stats, stringr, tibble, tidyr, utils, zlibbioc
LinkingTo Rcpp
Suggests DSS, Mus.musculus, Homo.sapiens, knitr, rmarkdown
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_1.0.0.tar.gz
Windows Binary NanoMethViz_1.0.0.zip
macOS 10.13 (High Sierra) NanoMethViz_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/NanoMethViz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NanoMethViz
Package Short Url https://bioconductor.org/packages/NanoMethViz/
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