This repository accompanies the paper chromswitch: A flexible method for detecting chromatin state switches (Selin Jessa and Claudia L. Kleinman).
A report of the complete analysis: https://sjessa.github.io/chromswitch-analysis/analysis.html.
That's simply a rendered version of the analysis.html file in this repository, which is generated by analysis.Rmd. The R Markdown document contains the code to download the data, run experiments, and generate the figures included in the paper, along with some notes and comments. The introduction of the HTML document details the contents of this repository and specifies how to reproduce the complete analysis.
chromswitch is an R/Bioconductor package which implements a flexible method to integrate epigenomic data to identify chromatin state switches in specific genomic regions of interest. It's available for download through Bioconductor 3.6 at http://bioconductor.org/packages/chromswitch/.