title: An interactive environment for agile analysis and visualization of ChIP-sequencing data.
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.
authors.affiliation: Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.|Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Mads
authors.initials: M
authors.lastname: Lerdrup
authors.affiliation: Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.|The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Jens Vilstrup
authors.initials: JV
authors.lastname: Johansen
authors.affiliation: Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.|Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Shuchi
authors.initials: S
authors.lastname: Agrawal-Singh
authors.affiliation: Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.|Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Klaus
authors.initials: K
authors.lastname: Hansen
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D016678:Genome; D051379:Mice; D063146:Polycomb-Group Proteins / Q000032:analysis; D012984:Software
chemical_list: D063146:Polycomb-Group Proteins