methylscaper

methylscaper is an R package for visualizing data that jointly profile endogenous methylation and chromatin accessibility (MAPit, NOMe-seq, scNMT-seq, nanoNOMe, etc.). The package offers pre-processing for single-molecule data and accepts input from Bismark (or similar alignment programs) for single-cell data. A common interface for visualizing both data types is constructed by generating ordered representational methylation-state matrices. The package provides a Shiny app to allow for interactive and optimal ordering of the individual DNA molecules to discover methylation patterns, nucleosome positioning, and transcription factor binding.

Webserver

methylscaper is available for use on a webserver located at www.methylscaper.com and clicking on "Start Shiny App". Also located on the website is easy access to the vignette and example datasets to use.

Installation

For local use of methylscaper, it can be installed into R from Bioconductor (using R version > 4.1.0):

```{r} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("methylscaper") ```

Alternatively, the version specified by the ref parameter below only requires R >= 4.0 (current stable release).

{r} if (!requireNamespace("devtools", quietly=TRUE)) install.packages("devtools") devtools::install_github("rhondabacher/methylscaper", ref="R4.0")

Development Setup

To contribute to this package, follow these steps after cloning the repository:

Run this command in bash git config core.hooksPath .hooks

Verify if the hooks are installed ls -la .hooks

If you encounter any issues with the pre-commit hooks - Ensure you've run the git config command as described above. - Check that the .hooks/pre-commit file is executable. If not, run: chmod +x .hooks/pre-commit

Dependencies

Note: on Ubuntu, users may need to install libgsl via: sudo apt-get install libgsl-dev

The following packages are required for methylscaper. If installation fails, you may need to manually install the dependencies using the function 'install.packages' for CRAN packages or 'BiocManager::install' for Bioconductor packages.

• CRAN packages: shiny, shinyjs, shinyFiles, seriation, seqinr, Rfast, data.table
• Bioconductor packages: BiocParallel, Biostrings, SummarizedExperiment

For any other installation issues/questions please leave a message on our Github Issues.

Manuscript

The methylscaper manuscript is now available at Bioinformatics.

Running methylscaper

To load the package into R:

{r} library(methylscaper)

To use methylscaper as a Shiny App: {r} methylscaper::methylscaper()

Many more details and examples on how to use the Shiny App or functions directly in R are located in the vignette:

• Vignette

Contact/Maintainer

• Rhonda Bacher (rbacher@ufl.edu)
  Department of Biostatistics, University of Florida