An interactive environment for agile analysis and visualization of ChIP-sequencing data
Research output: Contribution to journal › Journal article › Research › peer-review
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.
Original language | English |
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Journal | Nature Structural and Molecular Biology |
Volume | 23 |
Issue number | 4 |
Pages (from-to) | 349-57 |
Number of pages | 9 |
ISSN | 1545-9993 |
DOIs | |
Publication status | Published - Apr 2016 |
- Animals, Chromatin Immunoprecipitation, Genome, Mice, Polycomb-Group Proteins, Software, Journal Article, Research Support, Non-U.S. Gov't
Research areas
ID: 166015675