Name Mode Size
.github 040000
R 040000
inst 040000
man 040000
src 040000
tests 040000
vignettes 040000
.Rbuildignore 100644 0 kb
.covrignore 100644 0 kb
.gitignore 100644 0 kb
.lintr 100644 0 kb
DESCRIPTION 100644 2 kb
LICENSE.md 100644 10 kb
NAMESPACE 100644 4 kb
NEWS.md 100644 8 kb
README.md 100644 2 kb
_pkgdown.yml 100644 2 kb
codecov.yml 100644 0 kb
README.md
# NanoMethViz <!-- badges: start --> [![Codecov test coverage](https://codecov.io/gh/Shians/NanoMethViz/branch/master/graph/badge.svg)](https://codecov.io/gh/Shians/NanoMethViz?branch=master) [![R-CMD-check](https://github.com/Shians/NanoMethViz/workflows/R-CMD-check/badge.svg)](https://github.com/Shians/NanoMethViz/actions) <!-- badges: end --> NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. ## Installation You can install NanoMethViz from Bioconductor with: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("NanoMethViz") ``` To install the latest developmental version, use: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version='devel') BiocManager::install("NanoMethViz") ``` ## Usage This package currently works with data from dorado, megalodon, nanopolish and f5c, for information on how to use the package, please refer to the [Users Guide](https://www.bioconductor.org/packages/release/bioc/vignettes/NanoMethViz/inst/doc/UsersGuide.html). ## Examples ### MDS Plot The MDS plot is used to visualise differences in the methylation profiles of multiple samples. ![](man/figures/mds.png) ### Feature Aggregation The feature aggregation plot can average the methylation profiles across a set of features. ![](man/figures/agg_genes.png) ### Region Methylation Plot The region methylation plot can visualise the methylation profile of a region of interest. As well as provide a heatmap of the methylation along individual reads. ![](man/figures/peg3_gene.png) ## License This project is licensed under Apache License, Version 2.0.