NanoMethViz
Visualise methylation data from Oxford Nanopore sequencing
Bioconductor version: 3.24 · Package version: 3.9.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("NanoMethViz")Details
| Maintainer | Shian Su <su.s@wehi.edu.au> |
| Author | Shian Su [cre, aut] |
| License | Apache License (>= 2.0) |
| URL | https://github.com/shians/NanoMethViz, https://shians.github.io/NanoMethViz/ |
| Bug Reports | https://github.com/Shians/NanoMethViz/issues |
| System Requirements | C++20 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, LongRead, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/NanoMethViz/ |
Citation
From within R, enter citation("NanoMethViz"):
Shian Su. NanoMethViz: Visualise methylation data from Oxford Nanopore sequencing. doi:10.18129/B9.bioc.NanoMethViz, R package version 3.9.1, https://bioconductor.org/packages/NanoMethViz.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | NanoMethViz_3.9.1.tar.gz |
| Windows binary (x86_64) | NanoMethViz_3.9.1.zip |
| macOS binary (arm64) | NanoMethViz_3.9.1.tgz |
| macOS binary (x86_64) | NanoMethViz_3.9.1.tgz |
Dependencies
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
LinkingTo: Rcpp
Suggests: BiocStyle, 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