Welcome to the EpiChIP website


Daniel Hebenstreit1, Muxin Gu1, Syed Haider2, Daniel Turner3, Pietro Lio2, Sarah Teichmann1
1 Laboratory of Molecular Biology, Medical Research Council, 2 Computer Laboratory, University of Cambridge, 3 Wellcome Trust Sanger Institute


What does EpiChIP do?

EpiChIP is a software for analysing ChIP-sequencing data. It is mainly geared towards analysis of epigenetic modifications such as histone modifications. EpiChIP performs two major tasks:

Firstly, it searches for commonalities in sequencing read-enrichment according to known genomic marks (e.g. genes, exons, introns) and quantitatively identifies the "windows" of epigenetic modification. Subsequently, a gene-by-gene scoring may be performed to obtain an indication of the level of epigenetic modification for each gene.

Secondly, in the case that the epigenetic modification population consists of a mixture of two distributions (noise and signal), EpiChIP provides a Maximum Likelihood Estimation based method to identify the types of distributions and the parameters of each distribution and hence separate the noise from signal with a user-defined False Discovery Rate.

As an option, the epigenetic modification data can be linked to gene expression data (user supplied) and their relation can be visualised in a 2D heat map.

EpiChIP provides users with the most commonly used gene annotation files, which can be downloaded from the software. Users can generate their own gene annotation files with the AutoGen.jar module.

Download EpiChIP

Other things you may want to know:

If this is your first time using EpiChIP, I would suggest you spend 5 minutes going through the Quick Start Tutorial before getting on with your own data. Once you have been familiar with EpiChIP, you might want to know how technical details work behind GUI, you may find them in the documentation. If you need more Gene Annotation files you may download them from "File-> Download Gene Annotations" in the software. If there are still problems that the website did not answer, please contact us. We will be very glad to help.

Finally, we would be very pleased if you could send us constructive comments. Please feel free to contact us.

Funding: The project is funded by Medical Research Council