ChIP-seq (short course)

The Course

This course introduces some of the fundamental concepts and tools of ChIP-seq analysis in R/Bioconductor. This course is a shortened version of our full course and covers downstream analysis of ChIP-seq following peak calling and aquisition of QC results.

The course consists of 7 sections.

Evaluation of ChIP-seq specific QC metrics
Working with peaks.
Functional annotation of peaks.
Motif identification.
External/Public datasets.
Exporting data.
Complex overlaps.
Simple differential ChIP-seq.

Each section is presented as both HTMl and Rpres markdown ( to allow for intergration of the presentation in the RStudio enviroment itself). Exercises and answer sheets are included after all subsections to practice techniques and provide future reference examples.

Course material and exercises are available to view as rendered HTML slides at https://github.com/LMSBioinformatics/LMS_ChIPseq_short/.
All material is available to download under GPL Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

For information on other courses run by our team see our website.

The Team

This course was created and conducted by the MRC London Institute of Medical Sciences (LMS) Bioinformatics Team at Imperial College London, Hammersmith Hospital.
For more information on the team see our website.

This course is free for MRC LMS and Imperial staff and students. If you would like to attend a future course contact us.

Setting up.

Install R.

R can be installed from the R-project website.
R 3.1.0 or higher is required for this course.

http://www.r-project.org/

Install RStudio.

RStudio can be installed from the R-project website.

http://www.rstudio.com/

Install required packages.

Having downloaded R and RStudio, some additional packages are required (rmarkdown and ggplot2).
To install these,

First launch RStudio

Install the packages in the R console

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("GenomicRanges")
BiocManager::install("ChIPQC")
BiocManager::install("BSgenome.Mmusculus.UCSC.mm9")
BiocManager::install("ChIPseeker")
BiocManager::install("goseq")
BiocManager::install("rGREAT")
BiocManager::install("AnnotationHub")

Download the material

The material can either be downloaded as a zip

wget https://github.com/LMSBioinformatics/LMS_ChIPseq_short/archive/master.zip ./

or checked out from our Github repository https://github.com/LMSBioinformatics/LMS_ChIPseq_short/