methylscaper

DOI: 10.18129/B9.bioc.methylscaper    

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

Visualization of Methylation Data

Bioconductor version: Development (3.14)

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 "4.1") and enter:

if (!requireNamespace("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")

 

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 1.1.1
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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_1.1.1.tar.gz
Windows Binary methylscaper_1.1.1.zip
macOS 10.13 (High Sierra) methylscaper_1.1.1.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

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