22 May 2020 | Taiwen Li, Jingxin Fu, Zexian Zeng, David Cohen, Jing Li, Qianming Chen, Bo Li and X. Shirley Liu
TIMER2.0 is an improved web platform for analyzing tumor-infiltrating immune cells, offering more accurate and comprehensive estimation of immune infiltration levels using six state-of-the-art algorithms. It provides four modules for investigating associations between immune infiltrates and genetic or clinical features, and four modules for exploring cancer-related associations in TCGA cohorts. Each module generates a functional heatmap table, enabling users to easily identify significant associations in multiple cancer types simultaneously. TIMER2.0 also includes an 'estimation component' that allows users to infer immune infiltrates on their own expression profiles using multiple algorithms. The platform utilizes immunedeconv, an R package integrating six algorithms, including TIMER, xCell, MCP-counter, CIBERSORT, EPIC, and quanTIseq. These algorithms have been systematically benchmarked and each has unique properties and strengths. TIMER2.0 also supports mouse data analysis by converting mouse gene IDs to human gene IDs. The platform provides user-friendly visualization tools, including functional heatmap tables, violin plots, and Kaplan-Meier plots, to facilitate data exploration. TIMER2.0 is freely available at http://timer.cistrome.org. It is designed to help researchers analyze tumor immunity and its association with other tumor molecular and clinical features, providing insights into tumor-immune interactions and improving the understanding of cancer immunotherapy. The platform is supported by funding from various organizations, including the National Natural Science Foundation of China and the Cancer Prevention and Research Institute of Texas. The authors declare no competing interests.TIMER2.0 is an improved web platform for analyzing tumor-infiltrating immune cells, offering more accurate and comprehensive estimation of immune infiltration levels using six state-of-the-art algorithms. It provides four modules for investigating associations between immune infiltrates and genetic or clinical features, and four modules for exploring cancer-related associations in TCGA cohorts. Each module generates a functional heatmap table, enabling users to easily identify significant associations in multiple cancer types simultaneously. TIMER2.0 also includes an 'estimation component' that allows users to infer immune infiltrates on their own expression profiles using multiple algorithms. The platform utilizes immunedeconv, an R package integrating six algorithms, including TIMER, xCell, MCP-counter, CIBERSORT, EPIC, and quanTIseq. These algorithms have been systematically benchmarked and each has unique properties and strengths. TIMER2.0 also supports mouse data analysis by converting mouse gene IDs to human gene IDs. The platform provides user-friendly visualization tools, including functional heatmap tables, violin plots, and Kaplan-Meier plots, to facilitate data exploration. TIMER2.0 is freely available at http://timer.cistrome.org. It is designed to help researchers analyze tumor immunity and its association with other tumor molecular and clinical features, providing insights into tumor-immune interactions and improving the understanding of cancer immunotherapy. The platform is supported by funding from various organizations, including the National Natural Science Foundation of China and the Cancer Prevention and Research Institute of Texas. The authors declare no competing interests.