Xiaofan Lu1, Jialin Meng2, Yujie Zhou3, Liyun Jiang1,4, Fangrong Yan1. 1. State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China. 2. Department of Urology, The First Affiliated Hospital of Anhui Medical University; Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China. 3. Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. 4. Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Texas, USA.
Abstract
SUMMARY: Stratification of cancer patients into distinct molecular subgroups based on multi-omics data is an important issue in the context of precision medicine. Here we present MOVICS, an R package for multi-omics integration and visualization in cancer subtyping. MOVICS provides a unified interface for 10 state-of-the-art multi-omics integrative clustering algorithms, and incorporates the most commonly used downstream analyses in cancer subtyping researches, including characterization and comparison of identified subtypes from multiple perspectives, and verification of subtypes in external cohort using two model-free approaches for multiclass prediction. MOVICS also creates feature rich customizable visualizations with minimal effort. By analysing two published breast cancer cohort, we signifies that MOVICS can serve a wide range of users and assist cancer therapy by moving away from the 'one-size-fits-all' approach to patient care. AVAILABILITY AND IMPLEMENTATION: MOVICS package and online tutorial are freely available at https://github.com/xlucpu/MOVICS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Stratification of cancerpatients into distinct molecular subgroups based on multi-omics data is an important issue in the context of precision medicine. Here we present MOVICS, an R package for multi-omics integration and visualization in cancer subtyping. MOVICS provides a unified interface for 10 state-of-the-art multi-omics integrative clustering algorithms, and incorporates the most commonly used downstream analyses in cancer subtyping researches, including characterization and comparison of identified subtypes from multiple perspectives, and verification of subtypes in external cohort using two model-free approaches for multiclass prediction. MOVICS also creates feature rich customizable visualizations with minimal effort. By analysing two published breast cancer cohort, we signifies that MOVICS can serve a wide range of users and assist cancer therapy by moving away from the 'one-size-fits-all' approach to patient care. AVAILABILITY AND IMPLEMENTATION: MOVICS package and online tutorial are freely available at https://github.com/xlucpu/MOVICS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Xinjia Ruan; Yuqing Ye; Wenxuan Cheng; Li Xu; Mengjia Huang; Yi Chen; Junkai Zhu; Xiaofan Lu; Fangrong Yan Journal: Front Med (Lausanne) Date: 2022-06-03