Inference of biological pathway activity via gene set enrichment analysis is frequently used in the interpretation of clinical and other omics data. With the proliferation of new omics profiling approaches and ever-growing size of data sets generated, there is a lack of tools available to perform and visualise gene set enrichments in analyses involving multiple contrasts. To address this, we developed mitch, an R package for multi-contrast gene set enrichment analysis. It uses a rank-MANOVA statistical approach to identify sets of genes that exhibit joint enrichment across multiple contrasts. Its unique visualisation features enable the exploration of enrichments in up to 20 contrasts. We demonstrate the utility of mitch with case studies spanning multi-contrast RNA expression profiling, integrative multi-omics, tool benchmarking and single-cell RNA sequencing. Using simulated data we show that mitch has similar accuracy to state of the art tools for single-contrast enrichment analysis, and superior accuracy in identifying multi-contrast enrichments. mitch is a versatile tool for rapidly and accurately identifying and visualising gene set enrichments in multi-contrast omics data. Mitch is available from Bioconductor ( https://bioconductor.org/packages/mitch ).

中文翻译：

---

mitch：多组学和单细胞分析数据的多对比途径富集。

通过基因集富集分析推断生物途径活性经常用于解释临床和其他组学数据。随着新的组学分析方法的激增和生成的数据集规模的不断增长，在涉及多重对比的分析中缺乏可用于执行和可视化基因集富集的工具。为了解决这个问题，我们开发了 mitch，一个用于多对比基因集富集分析的 R 包。它使用排序多元方差分析统计方法来识别在多个对比中表现出联合富集的基因组。其独特的可视化功能可以探索多达 20 个对比的丰富内容。我们通过案例研究展示了 mitch 的实用性，涵盖多重对比 RNA 表达谱、综合多组学、工具基准测试和单细胞 RNA 测序。使用模拟数据，我们表明米奇在单对比富集分析方面具有与最先进的工具相似的准确性，并且在识别多对比富集方面具有出色的准确性。mitch 是一种多功能工具，用于快速准确地识别和可视化多对比组学数据中的基因集富集。Mitch 可从 Bioconductor (https://bioconductor.org/packages/mitch) 获取。