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Software Tools

We develop bioinformatic methods and software that address the needs of wet-lab researchers working on epigenetics and epigenomics. Most of this work is performed in collaboration with researchers at the Max Planck Institute for Informatics.

  • BiQ Analyzer (http://biqanalyzer.computational-epigenetics.org) is the most widely used tool for analyzing DNA methylation data from locus-specific bisulfite sequencing. The software comes in two versions: for Sanger sequencing and for next generation sequencing. Usage statistics: 7,000 users, 75,300 analyses since 2005.

  • EpiGRAPH (http://epigraph.mpi-inf.mpg.de) helps biologists analyze genome and epigenome datasets in a quantitative fashion with statistical learning methods. This tool is often used to predict the epigenetic and regulatory status of genomic regions. Usage statistics: 2,800 users, 131,300 page views since 2007. 

  • EpiExplorer (http://epiexplorer.mpi-inf.mpg.de) empowers biologists to explore large epigenome datasets interactively over the Internet. It facilitates hypothesis generation and identification of candidate genomic regions for experimental follow-up. Usage statistics: 3,300 users, 118,500 page views since 2012.

  • LOLA (http://lola.computational-epigenetics.org/) provides easy, automatable enrichment analysis for genomic region sets, thus facilitating the interpretation of functional genomics and epigenomics data. Launched in May 2015.

  • MethMarker (http://methmarker.mpi-inf.mpg.de) facilitates the design of DNA methylation assays for MSP, COBRA, bisulfite SNuPE, bisulfite pyrosequencing and MethyLight. It implements a systematic workflow epigenetic biomarker development. Usage statistics: 400 users, 2,100 analyses since 2008.

  • RnBeads (http://rnbeads.computational-epigenetics.org) was the first software tool that implements a comprehensive workflow for analyzing DNA methylation data in the context of large cohort studies. The main result is a detailed reports with production-quality graphics. Usage statistics: 1,950 users since 2014.

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

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