methylscaper
This is the released version of methylscaper; for the devel version, see methylscaper.
Visualization of Methylation Data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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_1.20.0.tar.gz |
| Windows Binary (x86_64) | methylscaper_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | methylscaper_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | methylscaper_1.20.0.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 3.23 | Source Archive |