UCSCXenaShiny：一个用于交互式分析 UCSC Xena 数据的 R/CRAN 包。

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

机构信息

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

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

出版信息

Bioinformatics. 2022 Jan 3;38(2):527-529. doi: 10.1093/bioinformatics/btab561.

DOI:10.1093/bioinformatics/btab561

PMID:34323947

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8723150/

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.

摘要

UCSC Xena 平台提供了大量来自大型癌症研究项目（如 TCGA、CCLE 和 PCAWG）或个别研究小组的已处理癌症组学数据，为研究提供了前所未有的机会。然而，仍然缺乏基于图形用户界面的工具来交互式分析 UCSC Xena 数据并生成优雅的图，特别是对于编程经验有限的癌症研究人员和临床医生。在这里，我们介绍了 UCSCXenaShiny，这是一个用于快速搜索、下载、探索、分析和可视化 UCSC Xena 数据中心数据的 R Shiny 包。该工具可以有效地促进公共数据的实际应用，并且可以作为当前 Xena 基因组学资源管理器的重要补充。