癌症中的基因组规模筛选实验会产生长长的候选基因列表，需要进行深入解读以获得生物学的洞察力，并为后续研究进行优先排序。解读基因列表通常是一个耗时且需要大量工作的过程，在这个过程中，实验生物学家通常会结合来自各种生物信息学资源的结果，以试图描绘和理解癌症的相关性。为了简化和加强这一努力的支持，我们开发了oncoEnrichR，这是一个灵活的生物信息学工具，允许癌症研究人员全面地探究给定基因列表与癌症相关性的多个方面。oncoEnrichR通过整合与癌症特异相关的大量先验知识，包括排名的基因-肿瘤类型关联、受文献支持的原癌基因和肿瘤抑制基因的注释、靶标可药性数据、调控相互作用、合成致死性预测，以及对肿瘤类型的预后相关、基因异常和共表达模式。该软件的主要输出是结构化和用户友好的分析报告，其中明确记录了所有底层数据资源的版本，后者是可复现科学的关键组成部分。我们通过对蛋白质组学和CRISPR筛选的两个候选列表的深入分析证明了oncoEnrichR的实用性。oncoEnrichR作为一个基于Galaxy平台（https://oncotools.elixir.no）提供的网络服务，可以免费获取，也可以作为一个独立的R包（https://github.com/sigven/oncoEnrichR）进行访问。© 2023 The Authors. International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.

Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typically combine results from a variety of bioinformatics resources in an attempt to portray and understand cancer relevance. As a means to simplify and strengthen the support for this endeavor, we have developed oncoEnrichR, a flexible bioinformatics tool that allows cancer researchers to comprehensively interrogate a given gene list along multiple facets of cancer relevance. oncoEnrichR differs from general gene set analysis frameworks through the integration of an extensive set of prior knowledge specifically relevant for cancer, including ranked gene-tumor type associations, literature-supported proto-oncogene and tumor suppressor gene annotations, target druggability data, regulatory interactions, synthetic lethality predictions, as well as prognostic associations, gene aberrations and co-expression patterns across tumor types. The software produces a structured and user-friendly analysis report as its main output, where versions of all underlying data resources are explicitly logged, the latter being a critical component for reproducible science. We demonstrate the usefulness of oncoEnrichR through interrogation of two candidate lists from proteomic and CRISPR screens. oncoEnrichR is freely available as a web-based service hosted by the Galaxy platform (https://oncotools.elixir.no), and can also be accessed as a stand-alone R package (https://github.com/sigven/oncoEnrichR).© 2023 The Authors. International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.