Software - Computational Epigenetics

We develop bioinformatic methods and software that address the needs of wet-lab researchers working on epigenetics / epigenomics. Your feedback on the existing tools (see below) as well as requests for novel methods and tools are highly appreciated (please contact Christoph Bock for further discussion).

BiQ Analyzer Logo

BiQ Analyzer ( is a software tool for easy visualization and quality control of DNA methylation data. With more than 2,000 downloads so far, BiQ Analyzer has become a standard tool for processing DNA methylation data from bisulfite sequencing. BiQ Analyzer has been selected by ABI to be part of the Applied Biosystems Software Community Program.

biq-analyzer-ht Logo

BiQ Analyzer HT ( is an enhanced version of BiQ Analyzer that provides extensive support for high-throughput bisulfite sequencing. It was developed for deep bisulfite sequencing of one or more loci using the Roche 454 platform, but it easily extends to other sequencing platforms. Users of clonal bisulfite sequencing who do not need these new features are encouraged to keep using the classical BiQ Analyzer.


EpiGRAPH ( enables biologists to analyze genome and epigenome datasets with powerful statistical and machine learning methods. In a typical workflow, the user uploads a set of genomic regions of interest (e.g. experimentally mapped enhancers, hotspots of epigenetic regulation or sites exhibiting disease-specific alterations), and EpiGRAPH searches a large database of (epi-) genomic attributes for significant overlap and correlation with the regions in the input dataset. Furthermore, EpiGRAPH can predict the status of genomic regions that were not included in the input dataset.

EpiExplorer Logo

EpiExplorer ( empowers biologists to explore large epigenome datasets in real time and over the Internet. It facilitates interactive hypothesis generation and identification of candidates for experimental follow-up.

MethMarker Logo

MethMarker ( facilitates the design of DNA methylation assays for COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight and MSP. It also implements a systematic workflow for design, optimization and (computational) validation of DNA methylation biomarkers. This workflow starts from a preselected differentially methylated region (DMR) and results in an optimized DNA methylation assay that is ready to be tested in a large-scale clinical trial.

RnBeads Logo

RnBeads ( is the first software tool that implements a comprehensive workflow for analyzing DNA methylation data in the context of large cohort studies. Its functionality comprises data normalization, quality control, probe and sample filtering, handing of batch effects, global DNA methylation analysis, detection of differentially methylated regions and interpretation by statistical enrichment analysis.

An overview of bioinformatic tools that are useful for epigenetic research are provided in our review papers on computational epigenetics and on the analysis and interpretation of DNA methylation data.