Differential Binding Analysis of ChIP-seq Experiments

DiffBind is an R package available in Bioconductor for the differential binding analysis of ChIP-seq experiments. It was developed by Rory Stark and Gord Brown in collaboration with Jason Carroll’s group.

DiffBind Workshop: Quantitative analysis of ChiP-seq, ATAC-seq, and related DNA enrichment assays

There is a workshop available, consisting of a R markdown script and associated data. This script walks through a complete example differential binding analysis using DiffBind. There are a variety of ways of running the workshop.

To run the practical in a local R session (550Mb download):

 R CMD INSTALL QuantitativeChIPseqWorkshop_0.1.2.tar.gz
  • Run R (preferably in RStudio)

To run the practical in a Docker session (9Gb download):

  1. docker pull crukcibioinformatics/quantitative_chip_workshop
  2. docker run -e PASSWORD=DiffBind -p 8888:8787   crukcibioinformatics/quantitative_chip_workshop
  3. In a browser, open the URL localhost:8888. Log into RStudio with username:rstudio and password:DiffBind

Once you have an R session open:

  1. Load Packages
    • library(DiffBind)
    • library(QuantitativeChIPseqWorkshop)
  2. Navigate to the data directory:
setwd(paste(system.file("extdata", package="QuantitativeChIPseqWorkshop")))

There are a variety of ways to reference the workshop script:

vignette("Quantitative-ChIPseq-Workshop", "QuantitativeChIPseqWorkshop")
  • Tutorial rendered in RStudio viewer window:
rstudioapi::viewer(paste(system.file("doc",package="QuantitativeChIPseqWorkshop"), "Quantitative-ChIPseq-Workshop.html", sep="/"))
  • Tutorial markdown source in RStudio source editor pane:
file.edit(paste(system.file("doc",package="QuantitativeChIPseqWorkshop"), "Quantitative-ChIPseq-Workshop.Rmd", sep="/"))

Start following the script at the section entitled Loading an experiment into DiffBind“.

Link to video of workshop at EuroBioc 2020:

Other workshop links: