methylscaper

DOI: 10.18129/B9.bioc.methylscaper    

Visualization of Methylation Data

Bioconductor version: Release (3.15)

methylscaper is an R package for processing and visualizing data jointly profiling methylation and chromatin accessibility (MAPit, NOMe-seq, scNMT-seq, nanoNOMe, etc.). The package supports both single-cell and single-molecule data, and a common interface for jointly visualizing both data types through the generation of ordered representational methylation-state matrices. The Shiny app allows for an interactive seriation process of refinement and re-weighting that optimally orders the cells or DNA molecules to discover methylation patterns and nucleosome positioning.

Author: Bacher Rhonda [aut, cre], Parker Knight [aut]

Maintainer: Bacher Rhonda <rbacher at ufl.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("methylscaper")

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("methylscaper")

 

HTML	R Script	Using methylscaper to visualize joint methylation and nucleosome occupancy data
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, Epigenetics, NucleosomePositioning, PrincipalComponent, SingleCell, Software, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 years)
License	GPL-2
Depends	R (>= 4.1.0)
Imports	shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment
LinkingTo
Suggests	knitr, rmarkdown, devtools
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	methylscaper_1.4.0.tar.gz
Windows Binary	methylscaper_1.4.0.zip (64-bit only)
macOS Binary (x86_64)	methylscaper_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methylscaper
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methylscaper
Package Short Url	https://bioconductor.org/packages/methylscaper/
Package Downloads Report	Download Stats