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.