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methylscaper

Visualization of Methylation Data


Bioconductor version: Release (3.18)

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: Rhonda Bacher <rbacher at ufl.edu>

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

Installation

To install this package, start R (version "4.3") 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")
Using methylscaper to visualize joint methylation and nucleosome occupancy data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, Epigenetics, NucleosomePositioning, Sequencing, SingleCell, Software, Visualization
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, devtools, R.utils
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Package Archives

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

Source Package methylscaper_1.10.0.tar.gz
Windows Binary methylscaper_1.10.0.zip
macOS Binary (x86_64) methylscaper_1.10.0.tgz
macOS Binary (arm64) methylscaper_1.10.0.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