Department of Medical Statistics, University Medical Center Göttingen, Göttingen 37099, Germany.
Discovery Science, Clarivate Analytics, Boston, MA 02210, USA.
Bioinformatics. 2018 Feb 15;34(4):716-717. doi: 10.1093/bioinformatics/btx683.
Seamless exchange of biological network data enables bioinformatic algorithms to integrate networks as prior knowledge input as well as to document resulting network output. However, the interoperability between pathway databases and various methods and platforms for analysis is currently lacking. The Network Data Exchange (NDEx) is an open-source data commons that facilitates the user-centered sharing and publication of networks of many types and formats.
Here, we present a software package that allows users to programmatically connect to and interface with NDEx servers from within R. The network repository can be searched and networks can be retrieved and converted into igraph-compatible objects. These networks can be modified and extended within R and uploaded back to the NDEx servers.
ndexr is a free and open-source R package, available via GitHub (https://github.com/frankkramer-lab/ndexr) and Bioconductor (http://bioconductor.org/packages/ndexr/).
florian.auer@med.uni-goettingen.de.
Supplementary data are available at Bioinformatics online.
生物网络数据的无缝交换使生物信息算法能够将网络集成作为先验知识输入，并记录生成的网络输出。然而，目前缺乏途径数据库与各种分析方法和平台之间的互操作性。网络数据交换（NDEx）是一个开源数据公共设施，它使用户能够在中心共享和发布多种类型和格式的网络。
在这里，我们介绍了一个软件包，允许用户从 R 内部编程连接到和与 NDEx 服务器进行接口。可以搜索网络存储库，检索网络并将其转换为igraph 兼容的对象。可以在 R 内部修改和扩展这些网络，并将其上传回 NDEx 服务器。
ndexr 是一个免费的开源 R 包，可通过 GitHub（https://github.com/frankkramer-lab/ndexr）和 Bioconductor（http://bioconductor.org/packages/ndexr/）获得。
florian.auer@med.uni-goettingen.de。
补充数据可在 Bioinformatics 在线获得。
