UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data

Author:

Wang Shixiang123ORCID,Xiong Yi456,Zhao Longfei7,Gu Kai8,Li Yin9,Zhao Fei310,Li Jianfeng1112,Wang Mingjie11,Wang Haitao13,Tao Ziyu1,Wu Tao1,Zheng Yichao7,Li Xuejun45,Liu Xue-Song1ORCID

Affiliation:

1. School of Life Science and Technology, ShanghaiTech University, 201203 Shanghai, China

2. Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 200031 Shanghai, China

3. University of Chinese Academy of Sciences, 100049 Beijing, China

4. Department of Neurosurgery, Xiangya Hospital, Central South University, 410008 Changsha, China

5. Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, 410008 Changsha, China

6. Xiangya School of Medicine, Central South University, 410013 Changsha, China

7. School of Pharmaceutical Sciences, Zhengzhou University, 450001 Zhengzhou, China

8. Roche Diagnostics (Shanghai) Limited, 201107 Shanghai, China

9. Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 200032 Shanghai, China

10. CAS Center for Excellence in Molecular Plant Sciences, 200032 Shanghai, China

11. State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University, School of Medicine, 200025 Shanghai, China

12. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China

13. Center for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, 999087 Macau SAR, China

Abstract

Abstract Summary UCSC Xena platform provides huge amounts of processed cancer omics data from large cancer research projects (e.g. TCGA, CCLE and PCAWG) or individual research groups and enables unprecedented research opportunities. However, a graphical user interface-based tool for interactively analyzing UCSC Xena data and generating elegant plots is still lacking, especially for cancer researchers and clinicians with limited programming experience. Here, we present UCSCXenaShiny, an R Shiny package for quickly searching, downloading, exploring, analyzing and visualizing data from UCSC Xena data hubs. This tool could effectively promote the practical use of public data, and can serve as an important complement to the current Xena genomics explorer. Availability and implementation UCSCXenaShiny is an open source R package under GPLv3 license and it is freely available at https://github.com/openbiox/UCSCXenaShiny or https://cran.r-project.org/package=UCSCXenaShiny. The docker image is available at https://hub.docker.com/r/shixiangwang/ucscxenashiny. Supplementary information Supplementary data are available at Bioinformatics online.

Funder

National Natural Science Foundation of China

Shanghai Science and Technology Commission

ShanghaiTech University

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

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