NanoMethViz
Bioc currentVisualise methylation data from Oxford Nanopore sequencing
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
232 40 exported
Complexity
2.5 avg / 13 max
Call network
232 nodes / 247 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
11,416
Files
172
Compiled share
17.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
53
Internal functions
119
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.19
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
11.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.0
System requirements
1 externalC++20
C++ standard
–
License
Apache License (>= 2.0)
License flags
not SPDX, not OSI
History
Versions
12
First release
2020-10-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
17
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 53 (18 internal)includes a package overview page
- Examples that run
- 100%31 run in a plain check
- Exported functions with examples
- 74%
- Documented parameters
- 79%
- Return-value docs
- 81%
- Help pages citing references
- 0%
- User's Guide HTML
- Addes sorting to the heatmap so reads appear from most to least methylated. This is done by calculating the average methylation across the region for each read and sorting by this value.
From NEWS.md in the release
Repository practices
9 development-tooling and community-health practices detected across 5 families in the upstream repository
Checks run against github.com/shians/nanomethviz on 2026-10-11.
The R CMD check workflow runs on Linux and Windows, and on R-devel
GitHub Pages site last deployed 2026-10-07 · The repository has a site deploy workflow
pkgdown site last built 2026-10-07
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Topics
Depended on by (1)
Bioconductor (1)
People
- Shian Su maintainer author
Cite
Cite this package
Run in R for the authors' entry:
citation("NanoMethViz")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1371/journal.pcbi.1009524.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.