Apple may have bombed their latest Maps integration, but the Epigenome mapping consortia out there are making it look easy by pumping out datasets by the server full. So it only makes sense that there needs to be robust software to help researchers make sense of it all. Two new papers in Genome Biology offer up some data analysis solutions to help epigenetics scientists dig themselves out from under all those mountains of information.
EpiExplorer: Interactive Epigenomic Data Browser
A team of scientists at the Max Planck Institute for Informatics has created a new tool called EpiExplorer, which is a web tool for exploring genome and epigenome data on a genomic scale.
EpiExplorer is modeled after web search engines, and unlike other genome browsers, uses an interactive filter-and-refine workflow. EpiExplorer conducts its searches by dynamically filtering genomic region sets and providing instant graphical results summaries. Also, just like your favorite web browser, EpiExplorer is highly fault-tolerant, and it allows users to adjust any aspect of an analysis (like thresholds or filtering criteria) at any time without having to repeat previous the query. You can find the EpiExplorer software available at http://epiexplorer.mpi-inf.mpg.de. Or learn more about EpiExplorer at Genome Biology, Halachev et. al October 2012.
methylKit: DNA Methylation Data Analysis Toolkit
Researchers at Weill Cornell Medical College put together a package of tools and analysis algorithms called methylKit, which the team says is an “open-source, multi-threaded R package that can be used for any base-level dataset of DNA methylation or base modifications, including 5hmC.
In this Genome Biology paper methylKit was tested out using breast cancer RRBS samples to demonstrate its capability to rapidly analyze genome-wide profiles from high-throughput methylation and hydroxymethylation sequencing experiments. methylKit boasts several functions that automate and make life easier for researchers analyzing DNA mehylation including:
- Sample quality visualization
- Differential methylation analysis and