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):
- Download workshop package: QuantitativeChIPseqWorkshop_0.1.2.tar.gz
- Run R
-
BiocManager::install("DiffBind") -
Command line:
R CMD INSTALL QuantitativeChIPseqWorkshop_0.1.2.tar.gz
- Run R (preferably in RStudio)
To run the practical in a Docker session (9Gb download):
-
docker pull crukcibioinformatics/quantitative_chip_workshop
-
docker run -e PASSWORD=DiffBind -p 8888:8787 crukcibioinformatics/quantitative_chip_workshop
- In a browser, open the URL localhost:8888. Log into RStudio with username:rstudio and password:DiffBind
Once you have an R session open:
- Load Packages
-
library(DiffBind) -
library(QuantitativeChIPseqWorkshop)
-
- Navigate to the data directory:
setwd(paste(system.file("extdata", package="QuantitativeChIPseqWorkshop")))
There are a variety of ways to reference the workshop script:
- Tutorial rendered in separate tab: Work through HTML script
- Tutorial markdown source in separate tab: Work through markdown script
- Tutorial rendered in RStudio help pane:
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“.