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# 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 []( 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") ``` # 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 A preprint of the methylscaper manuscript is now available on [bioRxiv]( # 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]( ( Department of Biostatistics, University of Florida