methylscaper
Visualization of Methylation Data
Bioconductor version: 3.23 · Package version: 1.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("methylscaper")Details
| Maintainer | Bacher Rhonda <rbacher@ufl.edu> |
| Author | Bacher Rhonda [aut, cre], Parker Knight [aut] |
| License | GPL-2 |
| URL | https://github.com/rhondabacher/methylscaper/ |
| Bug Reports | https://github.com/rhondabacher/methylscaper/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, Epigenetics, NucleosomePositioning, Sequencing, SingleCell, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/methylscaper/ |
Citation
From within R, enter citation("methylscaper"):
Bacher Rhonda, Parker Knight. methylscaper: Visualization of Methylation Data. doi:10.18129/B9.bioc.methylscaper, R package version 1.20.0, https://bioconductor.org/packages/methylscaper.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | methylscaper_1.20.0.tar.gz |
| Windows binary (x86_64) | methylscaper_1.20.0.zip |
| macOS binary (arm64) | methylscaper_1.20.0.tgz |
| macOS binary (x86_64) | methylscaper_1.20.0.tgz |
Dependencies
Depends: R (>= 4.4.0)
Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment