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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.

Author information

1
Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
2
Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark.
3
The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

Abstract

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.

PMID:
26926434
DOI:
10.1038/nsmb.3180
[Indexed for MEDLINE]

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