CEPICS: A Comparison and Evaluation Platform for Integration Methods in Cancer Subtyping

Duan, Ran and Gao, Lin and Xu, Han and Song, Kuo and Hu, Yuxuan and Wang, Hongda and Dong, Yongqiang and Zhang, Chenxing and Jia, Songwei (2019) CEPICS: A Comparison and Evaluation Platform for Integration Methods in Cancer Subtyping. Frontiers in Genetics, 10. ISSN 1664-8021

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Abstract

Cancer subtypes can improve our understanding of cancer, and suggest more precise treatment for patients. Multi-omics molecular data can characterize cancers at different levels. Up to now, many computational methods that integrate multi-omics data for cancer subtyping have been proposed. However, there are no consistent criteria to evaluate the integration methods due to the lack of gold standards (e.g., the number of subtypes in a specific cancer). Since comprehensive evaluation and comparison between different methods serves as a useful tool or guideline for users to select an optimal method for their own purpose, we develop a scalable platform, CEPICS, for comprehensively evaluating and comparing multi-omics data integration methods in cancer subtyping. Given a user-specified maximum number of subtypes, k-max, CEPICS provides (1) cancer subtyping results using up to five built-in state-of-the-art integration methods under the number of subtypes from two to k-max, (2) a report including the evaluation of each user-selected method and comparisons across them using clustering performance metrics and clinical survival analysis, and (3) an overall analysis of subtyping results by different methods representing a robust cancer subtype prediction for samples. Furthermore, users can upload subtyping results of their own methods to compare with the built-in methods. CEPICS is implemented as an R package and is freely available at https://github.com/GaoLabXDU/CEPICS.

Item Type: Article
Subjects: STM Digital Press > Medical Science
Depositing User: Unnamed user with email support@stmdigipress.com
Date Deposited: 08 Feb 2023 08:55
Last Modified: 22 Aug 2024 13:01
URI: http://publications.articalerewriter.com/id/eprint/212

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