UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data

doi:10.1093/bioinformatics/btab561

	UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data
	Wang, Shixiang1,2,3 ; Xiong, Yi 4,5,6; Zhao, Longfei 7; Gu, Kai 8; Li, Yin 9; Zhao, Fei 3,10; Li, Jianfeng 11,12; Wang, Mingjie 11; Wang, Haitao 13; Tao, Ziyu1 ; Wu, Tao1 ; Zheng, Yichao 7; Li, Xuejun 4,5; Liu, Xue-Song1
	2021-07
发表期刊	BIOINFORMATICS (IF:4.4[JCR-2023],7.6[5-Year])
ISSN	1367-4803
EISSN	1460-2059
卷号	38 期号:2
发表状态	已发表
DOI	10.1093/bioinformatics/btab561
摘要	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 (GUI) 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. Contact: Xue-Song Liu, liuxs@shanghaitech.edu.cn; Xuejun Li, lxjneuro@csu.edu.cn. Supplementary Information: Supplementary data are available at Bioinformatics online.
关键词	Cancer genome UCSC Xena UCSCXenaShiny Genome visualization
URL	查看原文
收录类别	SCI ; SCIE
语种	英语
资助项目	National Natural Science Foundation of China[31771373,81472594,81770781] ; Shanghai Science and Technology Commission[21ZR1442400]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000743380100030
出版者	OXFORD UNIV PRESS
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/127764
专题	生命科学与技术学院_博士生生命科学与技术学院_PI研究组_刘雪松组
通讯作者	Li, Xuejun; Liu, Xue-Song
作者单位	1.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201203, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Biochem & Cell Biol, Shanghai 200031, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Cent South Univ, Xiangya Hosp, Dept Neurosurg, Changsha 410008, Peoples R China 5.Cent South Univ, Xiangya Hosp, Hunan Int Sci & Technol Cooperat Base Brain Tumor, Changsha 410008, Peoples R China 6.Cent South Univ, Xiangya Sch Med, Changsha 410013, Peoples R China 7.Zhengzhou Univ, Sch Pharmaceut Sci, Zhengzhou 450001, Peoples R China 8.Roche Diagnost Shanghai Ltd, Shanghai 201107, Peoples R China 9.Fudan Univ, Zhongshan Hosp, Dept Thorac Surg, Shanghai 200032, Peoples R China 10.CAS Ctr Excellence Mol Plant Sci, Shanghai 200032, Peoples R China 11.Shanghai Jiao Tong Univ, Rui Jin Hosp, Natl Res Ctr Translat Med, State Key Lab Med Genom,Sch Med,Shanghai Inst Hem, Shanghai 200025, Peoples R China 12.Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Shanghai 200240, Peoples R China 13.Univ Macau, Fac Hlth Sci, Ctr Precis Med Res & Training, Macau 999087, Peoples R China
第一作者单位	生命科学与技术学院
通讯作者单位	生命科学与技术学院
第一作者的第一单位	生命科学与技术学院
推荐引用方式 GB/T 7714	Wang, Shixiang,Xiong, Yi,Zhao, Longfei,et al. UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data[J]. BIOINFORMATICS,2021,38(2).
APA	Wang, Shixiang.,Xiong, Yi.,Zhao, Longfei.,Gu, Kai.,Li, Yin.,...&Liu, Xue-Song.(2021).UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data.BIOINFORMATICS,38(2).
MLA	Wang, Shixiang,et al."UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data".BIOINFORMATICS 38.2(2021).