An interactive environment for agile analysis and visualization of ChIP-sequencing data
An interactive environment for agile analysis and visualization of ChIP-sequencing data
复制标题
DOI：
10.1038/nsmb.3180
复制
发表时间：
2016-04-01
影响因子：
16.8
通讯作者：
Hansen, Klaus
中科院分区：
文献类型：
--
作者：
Lerdrup, Mads;Johansen, Jens Vilstrup;Hansen, Klaus
为了使实验者有能力进行快速和全面的染色质免疫沉淀测序(CHIP-SEQ)数据分析，我们引入了一个集成的计算环境EaSeq。该软件结合了基因组浏览器的探索能力和一套广泛的交互式和用户友好的工具，用于全基因组的抽象和可视化。它使实验者能够轻松地提取信息，并从他们自己的数据和公开的全基因组数据集中生成假说。出于演示目的，我们对公共Polycomb芯片序列数据进行了荟萃分析，并建立了一种新的筛选方法来分析来自小鼠胚胎干细胞的900多个数据集，以寻找可能与Polycomb招募相关的因素。EaSeq是免费提供的，可以在标准的个人计算机上运行，它可以显著增加许多分析工作流程的吞吐量，通过自动记录和组织分析来促进透明度和重复性，并使更广泛的科学家群体能够从芯片序列数据中获得见解。
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.