Competitive endogenous RNA (ceRNA) represents a novel layer of gene regulation that controls both physiological and pathological processes. However, there is still lack of computational tools for quickly identifying ceRNA regulation. To address this problem, we presented an R-package, CeRNASeek, which allows identifying and analyzing ceRNA-ceRNA interactions by integration of multiple-omics data. CeRNASeek integrates six widely used computational methods to identify ceRNA-ceRNA interactions, including two global and four context-specific ceRNA regulation prediction methods. In addition, it provides several downstream analyses for predicted ceRNA-ceRNA pairs, including regulatory network analysis, functional annotation and survival analysis. With examples of cancer-related ceRNA prioritization and cancer subtyping, we demonstrate that CeRNASeek is a valuable tool for investigating the function of ceRNAs in complex diseases. In summary, CeRNASeek provides a comprehensive and efficient tool for identifying and analysis of ceRNA regulation. The package is available on the Comprehensive R Archive Network (CRAN) at https://CRAN.R-project.org/package=CeRNASeek.

中文翻译：

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CeRNASeek：用于识别和分析 ceRNA 调控的 R 包。

竞争性内源性 RNA (ceRNA) 代表了一个新的基因调控层，可以控制生理和病理过程。然而，仍然缺乏用于快速识别 ceRNA 调控的计算工具。为了解决这个问题，我们提出了一个 R 包，CeRNASeek，它允许通过整合多组学数据来识别和分析 ceRNA-ceRNA 相互作用。CeRNASeek 集成了六种广泛使用的计算方法来识别 ceRNA-ceRNA 相互作用，包括两种全局和四种上下文特定的 ceRNA 调控预测方法。此外，它还为预测的 ceRNA-ceRNA 对提供了几种下游分析，包括调节网络分析、功能注释和生存分析。以癌症相关的 ceRNA 优先级和癌症亚型为例，我们证明 CeRNASeek 是研究 ceRNA 在复杂疾病中的功能的宝贵工具。总之，CeRNASeek 为识别和分析 ceRNA 调控提供了一个全面而有效的工具。该软件包可在综合 R 档案网络 (CRAN) 上获得，网址为 https://CRAN.R-project.org/package=CeRNASeek。