Program in Computational Biology and Bioinformatics, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
Bioinformatics. 2011 Apr 15;27(8):1152-4. doi: 10.1093/bioinformatics/btr092. Epub 2011 Feb 23.
We have implemented aggregation and correlation toolbox (ACT), an efficient, multifaceted toolbox for analyzing continuous signal and discrete region tracks from high-throughput genomic experiments, such as RNA-seq or ChIP-chip signal profiles from the ENCODE and modENCODE projects, or lists of single nucleotide polymorphisms from the 1000 genomes project. It is able to generate aggregate profiles of a given track around a set of specified anchor points, such as transcription start sites. It is also able to correlate related tracks and analyze them for saturation--i.e. how much of a certain feature is covered with each new succeeding experiment. The ACT site contains downloadable code in a variety of formats, interactive web servers (for use on small quantities of data), example datasets, documentation and a gallery of outputs. Here, we explain the components of the toolbox in more detail and apply them in various contexts.
ACT is available at http://act.gersteinlab.org
我们已经实现了聚合和相关工具包（ACT），这是一个高效、多方面的工具包，可用于分析高通量基因组实验的连续信号和离散区域轨迹，例如来自 ENCODE 和 modENCODE 项目的 RNA-seq 或 ChIP-chip 信号谱，或来自 1000 基因组计划的单核苷酸多态性列表。它能够围绕一组指定的锚点（例如转录起始位点）生成给定轨迹的聚合谱。它还能够相关联的轨迹并分析它们的饱和度-即，每个新的后续实验覆盖了多少特定特征。ACT 网站提供了各种格式的可下载代码、交互式网络服务器（用于处理少量数据）、示例数据集、文档和输出画廊。在这里，我们更详细地解释了工具包的组件，并将它们应用于各种情况。
ACT 可在 http://act.gersteinlab.org 获得。
Zotero 插件