NanoMethViz
Visualise methylation data from Oxford Nanopore sequencing
Bioconductor version: Release (3.20)
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("NanoMethViz")):
Installation
To install this package, start R (version "4.4") 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")| User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, LongRead, Software, Visualization |
| Version | 3.2.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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, zlibbioc |
| 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.
| Source Package | NanoMethViz_3.2.0.tar.gz |
| Windows Binary (x86_64) | NanoMethViz_3.2.0.zip |
| macOS Binary (x86_64) | NanoMethViz_3.2.0.tgz |
| macOS Binary (arm64) | NanoMethViz_3.2.0.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 |