This tutorial is complementary to the protocol article:
Boeckel et al. ‘Differential Analysis of Protein-DNA Binding Using ChIP-Seq Data’. Chromatin Immunoprecipitation: Methods and Protocols, edited by Franziska Greulich, Springer US, 2024, pp. 63–89, https://doi.org/10.1007/978-1-0716-4071-5_5.
Please install R and Rstudio. All required R packages can then be installed by running the 00_install_packages.R script in RStudio.
The tutorial can then be run by knitting the file ER_tutorial.Rmd in RStudio, which will download the required data, create a html report, the results tables and figures. An already knitted report is available from this repository (ER_tutorial.html).
Please note, this report has been generated with R version 4.2.2 and RStudio version 2023.03.1 Build 446.