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.
Illumina's HumanMethylation BeadChips
are enjoying increasing popularity and are widely used for the genome-wide DNA methylation profiling of epidemiological and clinical samples. Based on the bisulfite conversion and subsequent primer extension, these microarrays can yield quantitative DNA methylation estimates at single CpG resolution. Until recently no integrative data processing and analysis solutions existed that would be easy to use and comprehensive for the users with a life-science background. In cooperation with the Max-Planck Institute for Informatics Computational Biology department our group has now filled this gap. RnBeads
R-package is a turnkey pipeline which leads the user from raw input data of various formats, through numerous quality assessment, normalization and filtering steps to differentially methylated CpGs, promoters and genes. Multiple facets of data representation by RnBeads enable a deep and through understanding of the HumanMethylation450 data sets, and simplify the gain of valuable biological insights. Publication-quality graphics based on novel R-graphics grammar, and solid statistical methods in the background, make it much easier for life-science users to report on their results, without being swamped in creation of the custom bioinformatic solutions.