DOI: 10.18129/B9.bioc.methylscaper    

Visualization of Methylation Data

Bioconductor version: Release (3.13)

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>

Citation (from within R, enter citation("methylscaper")):


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HTML R Script Using methylscaper to visualize joint methylation and nucleosome occupancy data
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biocViews DNAMethylation, Epigenetics, NucleosomePositioning, PrincipalComponent, SingleCell, Software, Visualization
Version 1.0.0
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
Suggests knitr, rmarkdown, devtools
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