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Nat Struct Mol Biol. 2016 Apr;23(4):349-57. doi: 10.1038/nsmb.3180. Epub 2016 Feb 29.

An interactive environment for agile analysis and visualization of ChIP-sequencing data.

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Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark.
The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.


To empower experimentalists with a means for fast and comprehensive chromatin immunoprecipitation sequencing (ChIP-seq) data analyses, we introduce an integrated computational environment, EaSeq. The software combines the exploratory power of genome browsers with an extensive set of interactive and user-friendly tools for genome-wide abstraction and visualization. It enables experimentalists to easily extract information and generate hypotheses from their own data and public genome-wide datasets. For demonstration purposes, we performed meta-analyses of public Polycomb ChIP-seq data and established a new screening approach to analyze more than 900 datasets from mouse embryonic stem cells for factors potentially associated with Polycomb recruitment. EaSeq, which is freely available and works on a standard personal computer, can substantially increase the throughput of many analysis workflows, facilitate transparency and reproducibility by automatically documenting and organizing analyses, and enable a broader group of scientists to gain insights from ChIP-seq data.

[Indexed for MEDLINE]

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