NanoMethViz
Visualise methylation data from Oxford Nanopore sequencing
Bioconductor version: 3.23 · Package version: 3.8.0
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 |
| Downloads rank | 339 |
| Source branch | RELEASE_3_23 |
| biocViews | DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, LongRead, Software, Visualization |
Documentation
Download
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