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Bioconductor - NanoMethViz (development version)

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 (3.22)

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 "4.5") 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")

Details biocViews DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, LongRead, Software, Visualization Version 3.5.2 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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, dbscan, e1071, fs, GenomicRanges, Biostrings, ggrastr, glue, graphics, IRanges, limma(>= 3.44.0), patchwork, purrr, rlang, R.utils, Rsamtools, scales (>= 1.2.0), stats, stringr, tibble, tidyr, utils, withr System Requirements C++20 URL https://github.com/shians/NanoMethViz https://shians.github.io/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 Links To Me Build Report Build Report Package Archives

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

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