methylscaper
Visualization of Methylation Data
Bioconductor version: Release (3.20)
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("methylscaper")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | DNAMethylation, Epigenetics, NucleosomePositioning, Sequencing, SingleCell, Software, Visualization |
Version | 1.14.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
See More
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_1.14.0.tar.gz |
Windows Binary (x86_64) | methylscaper_1.14.0.zip (64-bit only) |
macOS Binary (x86_64) | methylscaper_1.14.0.tgz |
macOS Binary (arm64) | methylscaper_1.13.3.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 |