BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data from bisulfite sequencing.

Homepage

http://biq-analyzer.bioinf.mpi-inf.mpg.de

Relevant Publications

Bock, C., Reither, S., Mikeska, T., Paulsen, M., Walter, J. and Lengauer, T., BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. (2005)Bioinformatics, 21(21), pp.4067-4068.

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BiQ Analyzer HiMod is the major upgrade of the popular BiQAnalyzer HT tool specifically designed to aid the analysis of high-throughput bisulfite amplicon sequencing data. BiQ Analyzer HiMod currently allows to process an amount of bisulfite, oxidative bisulfite, Tet assisted bisulfite, chemical modification-assisted bisulfite or formyl chemical modification-assisted bisulfite sequencing reads obtained in one or several sequencing experiments.

Homepage

http://biq-analyzer-himod.bioinf.mpi-inf.mpg.de/

Relevant Publications

Lutsik P., Feuerbach L., Arand J., Lengauer T., Walter J. and Bock C (2011) BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Research (Full text).

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BiQAnalyzer HT is the major upgrade of the popular BiQAnalyzer tool specifically designed to aid the analysis of high-throughput bisulfite amplicon sequencing data. BiQAnalyzer HT currently allows to process an amount of bisulfite sequencing reads obtained in one or several bisulfite sequencing experiments.

Homepage

http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/

Relevant Publications

Becker D., Lutsik P., Ebert P., Lengauer T. and Walter J. (2014) BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives. Nucleic Acids Research (Full text).

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The DeepBlue Epigenomic Data Server provides a data access hub for large collections of epigenomic data. It organizes the data using controlled vocabularies and ontologies.

Homepage

http://deepblue.mpi-inf.mpg.de

Relevant Publications

Albrecht, F., List, M., Bock, C., & Lengauer, T. (2016). DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. Nucleic Acids Research.

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EpiExplorer is a web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborous preprocessing. EpiExplorer integrates multiple epigenetic and genetic annotations and makes them explorable via an interactive interface.

Homepage

http://epiexplorer.mpi-inf.mpg.de

Relevant Publications

Halachev, K., Bast, H., Albrecht, F., Lengauer, T., & Bock, C. (2012). EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biology, 13(10), R96.

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R package for comprehensive analysis of DNA methylation data obtained by Infinium microarrays and bisulfite sequencing protocols. RnBeads implements a series of QC steps and comprehensively outputs a number of analyses levels as annotated and readable hypertext report. RnBeads is the standard preparation tool for DNA-methylation data obtained by DEEP (German Epigenome Programme).

Homepage

http://rnbeads.mpi-inf.mpg.de/

Relevant Publications

Assenov, Y., Müller, F., Lutsik, P., Walter, J., Lengauer, T., & Bock, C. (2014). Comprehensive analysis of DNA methylation data with RnBeads. Nature Methods, 11(11), 1138–1140.

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