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Local deep bisulfite sequencing
BiQ Analyzer HiMod is the latest version of the popular interactive sequence analysis tool, designed for high-throughput targeted sequencing of 5-methylcytosine and its oxidized derivatives. BiQ HiMod facilitates processing and primary analysis of data obtained in standard targeted bisulfite sequencing experiments, as well as oxidative, Tet-assisted, chemical modification-assisted or formyl chemical modification-assisted bisulfite sequencing. The tool features substantially reworked graphical user interface, a number of new diagrams, and a new vector graphics engine.
BiQ Analyzer HiMod emerged as a result of the intensive cooperation with the Computational Biology Department at the Max-Planck Institute for Informatics.
More information on getting and using BiQ Analyzer HiMod can be found in the publication describing it and at the program web-site.
Bead array-based genome-wide analysis pipeline
Genome-wide DNA methylation profiling is increasingly used for epidemiological and comparative clinical studies. Besides sequencing based NGS approaches such as RRBS and WGBS, bead array system provided by several manifacturers such as the 450K and EPIC HumanMethylation BeadChips are the major data recources. All these methods yield quantitative DNA methylation estimates at single CpG resolution. RnBeads offers a comprehensive "R" based package for a multilevel customer tailored integrated processing of raw data and their deep analysis. The comprehensive package is easy to use for applicants with a life-science background and basic knowledge in R based program applicaitons. RnBeads was developed in our group in cooperation with the Max-Planck Institute for Informatics Computational Biology RnBeads . RnBeads pipelines can be used for NGS and array based data. The user is lead from raw input data of various formats, through numerous quality assessment, normalization and filtering steps to differentially methylated CpGs links to annotations and other interpretation tools. RnBeads furthermore allows to use modern "normalisation" approaches (such as ReFactor,..) to decompose and adjust complex methylome datasets. RnBeads generates multiple (user controlled) exploratory plots and generates publication-quality graphics in state of the art R-graphics. The solid statistical methods applied in the background, make it easy for life-science users to report on their results.
Decomposition of complex methylomes
MeDeCom is a computational method for decomposition of heterogeneous DNA methylomes. It applies matrix factorization with biologically motivated constratints and regularization to discover and quantify latent components in methylomes of multi-cellular samples.