CePa: an R package for finding significant pathways weighted by multiple network centralities
CePa: an R package for finding significant pathways weighted by multiple network centralities
复制标题
CePa：一个 R 包，用于查找由多个网络中心加权的重要路径
DOI：
10.1093/bioinformatics/btt008
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发表时间：
2013-03-01
期刊：
影响因子：
5.8
通讯作者：
Wang, Jin
中科院分区：
文献类型：
--
作者：
Gu, Zuguang;Wang, Jin
概括
CePa 是一个 R 包，旨在通过网络拓扑信息找到重要路径。与当前的通路富集工具相比，该软件包具有多个优点。首先，在分析网络时，以通路节点而不是单个基因作为基本单位，以满足基因必须构建成复合体才能保持正常功能的事实。其次，同时应用多个网络中心性，从不同方面衡量节点的重要性，以全面了解生物系统。 CePa 扩展了标准通路富集方法，其中包括过度代表性分析程序和基因集分析程序。 CePa已经在真实数据上得到了高性能的评估，它可以提供更多与当前生物问题直接相关的信息。
可用性
CePa 可在综合 R 存档网络 (CRAN) 上获取：http://cran.r-project.org/web/packages/CePa/
SUMMARY
CePa is an R package aiming to find significant pathways through network topology information. The package has several advantages compared with current pathway enrichment tools. First, pathway node instead of single gene is taken as the basic unit when analysing networks to meet the fact that genes must be constructed into complexes to hold normal functions. Second, multiple network centralities are applied simultaneously to measure importance of nodes from different aspects to make a full view on the biological system. CePa extends standard pathway enrichment methods, which include both over-representation analysis procedure and gene-set analysis procedure. CePa has been evaluated with high performance on real-world data, and it can provide more information directly related to current biological problems.
AVAILABILITY
CePa is available at the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/CePa/