Preprint Technical Note Version 1 Preserved in Portico This version is not peer-reviewed

UCSCXenaShiny: An R Package for Exploring and Analyzing UCSC Xena Public Datasets in Web Browser

Version 1 : Received: 7 July 2020 / Approved: 9 July 2020 / Online: 9 July 2020 (07:59:18 CEST)

A peer-reviewed article of this Preprint also exists.

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

Journal reference: Bioinformatics 2021
DOI: 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

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