methylscaper
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see methylscaper.
Visualization of Methylation Data
Bioconductor version: 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>
citation("methylscaper")):
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")| Using methylscaper to visualize joint methylation and nucleosome occupancy data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Epigenetics, NucleosomePositioning, PrincipalComponent, SingleCell, Software, Visualization |
| Version | 1.4.0 |
| 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 | |
| URL |
See More
| Suggests | knitr, rmarkdown, devtools |
| 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_1.4.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/methylscaper/ |
| Package Short Url | https://bioconductor.org/packages/methylscaper/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.15 | Source Archive |