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This is the development version of methylscaper; for the stable release version, see methylscaper.

Visualization of Methylation Data

Bioconductor version: Development (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: Rhonda Bacher <rbacher at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Using methylscaper to visualize joint methylation and nucleosome occupancy data HTML R Script
Reference Manual PDF


biocViews DNAMethylation, Epigenetics, NucleosomePositioning, Sequencing, SingleCell, Software, Visualization
Version 1.13.0
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, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment
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Suggests BiocStyle, knitr, rmarkdown, devtools, R.utils
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Follow Installation instructions to use this package in your R session.

Source Package methylscaper_1.13.0.tar.gz
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macOS Binary (x86_64) methylscaper_1.13.0.tgz
macOS Binary (arm64) methylscaper_1.13.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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