Shixiang Wang, Yi Xiong, Longfei Zhao, Kai Gu, Yin Li, Fei Zhao, Jianfeng Li, Mingjie Wang, Haitao Wang, Ziyu Tao, Tao Wu, Yichao Zheng, Xuejun Li, Xue-Song Liu, UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data, Bioinformatics, 2021;, btab561, https://doi.org/10.1093/bioinformatics/btab561
Shixiang Wang, Yi Xiong, Longfei Zhao, Kai Gu, Yin Li, Fei Zhao, Jianfeng Li, Mingjie Wang, Haitao Wang, Ziyu Tao, Tao Wu, Yichao Zheng, Xuejun Li, Xue-Song Liu, UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data, Bioinformatics, 2021;, btab561, https://doi.org/10.1093/bioinformatics/btab561
Shixiang Wang, Yi Xiong, Longfei Zhao, Kai Gu, Yin Li, Fei Zhao, Jianfeng Li, Mingjie Wang, Haitao Wang, Ziyu Tao, Tao Wu, Yichao Zheng, Xuejun Li, Xue-Song Liu, UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data, Bioinformatics, 2021;, btab561, https://doi.org/10.1093/bioinformatics/btab561
Shixiang Wang, Yi Xiong, Longfei Zhao, Kai Gu, Yin Li, Fei Zhao, Jianfeng Li, Mingjie Wang, Haitao Wang, Ziyu Tao, Tao Wu, Yichao Zheng, Xuejun Li, Xue-Song Liu, UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data, Bioinformatics, 2021;, btab561, https://doi.org/10.1093/bioinformatics/btab561
Abstract
Motivation: UCSC Xena platform provides huge amounts of processed cancer omics data from big public projects like TCGA or individual reserach groups for enabling unprecedented research opportunities. In 2019, we developed UCSCXenaTools, an R package for retrieval of UCSC Xena data. However, an easier dataset exploration and analysis tool is still lack, especially for researchers without programming experience. Results: We develop UCSCXenaShiny, an R Shiny package to quickly explore, download all datasets from UCSC Xena data hubs. In addiction, a module based analysis framework is constructed to analyze and visualize data. Availability: https://github.com/openbiox/UCSCXenaShiny or https://cran.r-project.org/package=UCSCXenaShiny.
Keywords
UCSC Xena, cancer genomics, TCGA
Subject
Medicine and Pharmacology, Oncology and Oncogenics
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.