Summary: Large-scale sequencing projects, such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), have accumulated a variety of high throughput sequencing and molecular profiling data, but it is still challenging to identify potentially causal genetic mutations in cancer as well as in other diseases in an automated fashion. We developed the NetBoxR package written in the R programming language, that makes use of the NetBox algorithm to identify candidate cancer-related processes. The algorithm makes use of a network-based approach that combines prior knowledge with a network clustering algorithm, obviating the need for and the limitation of functionally curated gene sets. A key aspect of this approach is its ability to combine multiple data types, such as mutations and copy number alterations, leading to more reliable identification of functional modules. We make the tool available in the Bioconductor R ecosystem for applications in cancer research and cell biology. Availability and implementation: The NetBoxR package is free and open-sourced under the GNU GPL-3 license R package available at https://www.bioconductor.org/packages/release/bioc/html/netboxr.html Contact: lium2@mskcc.org; aluna@jimmy.harvard.edu; sander.research@gmail.com Supplementary information: None

中文翻译：

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NetBoxR：通过R中的网络分析自动发现生物过程模块

简介：大规模测序项目，例如癌症基因组图谱（TCGA）和国际癌症基因组协会（ICGC），已经积累了各种高通量测序和分子谱数据，但是鉴定潜在的因果遗传基因仍是挑战。以自动化方式在癌症以及其他疾病中突变。我们开发了用R编程语言编写的NetBoxR软件包，该软件包利用NetBox算法来识别与癌症有关的候选过程。该算法利用了一种基于网络的方法，该方法将先验知识与网络聚类算法相结合，从而消除了对功能性基因集的需求和限制。这种方法的一个关键方面是它能够组合多种数据类型，例如突变和拷贝数变化，从而可以更可靠地识别功能模块。我们在Bioconductor R生态系统中提供了该工具，可用于癌症研究和细胞生物学。可用性和实施​​：NetBoxR软件包是免费的，并根据GNU GPL-3许可证R软件包开放源代码，该软件包可从https://www.bioconductor.org/packages/release/bioc/html/netboxr.html获得。联系人：lium2 @ mskcc .org; aluna@jimmy.harvard.edu; sander.research@gmail.com补充信息：无 lium2@mskcc.org; aluna@jimmy.harvard.edu; sander.research@gmail.com补充信息：无 lium2@mskcc.org; aluna@jimmy.harvard.edu; sander.research@gmail.com补充信息：无