Zhao Zhi, Zucknick Manuela, Aittokallio Tero
Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo N-0310, Norway.
Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Oslo N-0372, Norway.
Bioinform Adv. 2022 Sep 27;2(1):vbac073. doi: 10.1093/bioadv/vbac073. eCollection 2022.
Enrichment analysis has been widely used to study whether predefined sets of genes or other molecular features are over-represented in a ranked list associated with a disease or other phenotype. However, computational tools that perform enrichment analysis and visualization are usually limited to predefined sets available from public databases. To make such analyses more flexible, we introduce an R package, , which enables enrichment analyses among any ranked features and user-defined custom sets. For interactive visualization of multiple covariates, such as genes or other features, which are associated with multiple phenotypes and multiple sample groups, such as drug responses in various cancer types, illustrates all associations at a glance, hence explicitly indicating intersecting covariates between multiple phenotypic variables and between multiple sample groups.
The R package is available at https://CRAN.R-project.org/package=EnrichIntersect via an open-source MIT license. A package installation process is described on CRAN at https://cran.r-project.org/. A user-manual description of features and function calls can be found from the vignette of our package on CRAN.
富集分析已被广泛用于研究预定义的基因集或其他分子特征在与疾病或其他表型相关的排序列表中是否过度富集。然而，执行富集分析和可视化的计算工具通常仅限于公共数据库中可用的预定义集。为了使此类分析更加灵活，我们引入了一个R包，它能够在任何排序列特征和用户定义的自定义集之间进行富集分析。对于与多种表型和多个样本组（如各种癌症类型中的药物反应）相关的多个协变量（如基因或其他特征）的交互式可视化， 可以一目了然地展示所有关联，从而明确指示多个表型变量之间以及多个样本组之间的交叉协变量。
R包可通过开源的MIT许可在https://CRAN.R-project.org/package=EnrichIntersect获得。CRAN上的https://cran.r-project.org/ 描述了包的安装过程。从我们在CRAN上的包的 vignette 中可以找到功能和函数调用的用户手册描述。
