methylscaper

This is the development version of methylscaper; for the stable release version, see methylscaper.

Visualization of Methylation Data

Bioconductor version: Development (3.22)

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>

Citation (from within R, enter citation("methylscaper")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, Epigenetics, NucleosomePositioning, Sequencing, SingleCell, Software, Visualization
Version	1.17.0
In Bioconductor since	BioC 3.13 (R-4.1) (4.5 years)
License	GPL-2
Depends	R (>= 4.4.0)
Imports	shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment
System Requirements
URL	https://github.com/rhondabacher/methylscaper/
Bug Reports	https://github.com/rhondabacher/methylscaper/issues

Suggests	BiocStyle, knitr, rmarkdown, devtools, R.utils
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	methylscaper_1.17.0.tar.gz
Windows Binary (x86_64)	methylscaper_1.17.0.zip
macOS Binary (x86_64)	methylscaper_1.17.0.tgz
macOS Binary (arm64)	methylscaper_1.17.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methylscaper
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methylscaper
Bioc Package Browser	https://code.bioconductor.org/browse/methylscaper/
Package Short Url	https://bioconductor.org/packages/methylscaper/
Package Downloads Report	Download Stats