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UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data
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...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8723150/ https://www.ncbi.nlm.nih.gov/pubmed/34323947 http://dx.doi.org/10.1093/bioinformatics/btab561 |
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author | Wang, Shixiang Xiong, Yi Zhao, Longfei Gu, Kai Li, Yin Zhao, Fei Li, Jianfeng Wang, Mingjie Wang, Haitao Tao, Ziyu Wu, Tao Zheng, Yichao Li, Xuejun Liu, Xue-Song |
author_facet | Wang, Shixiang Xiong, Yi Zhao, Longfei Gu, Kai Li, Yin Zhao, Fei Li, Jianfeng Wang, Mingjie Wang, Haitao Tao, Ziyu Wu, Tao Zheng, Yichao Li, Xuejun Liu, Xue-Song |
author_sort | Wang, Shixiang |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8723150 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87231502022-01-05 UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data Wang, Shixiang Xiong, Yi Zhao, Longfei Gu, Kai Li, Yin Zhao, Fei Li, Jianfeng Wang, Mingjie Wang, Haitao Tao, Ziyu Wu, Tao Zheng, Yichao Li, Xuejun Liu, Xue-Song Bioinformatics Applications Notes 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. Oxford University Press 2021-07-29 /pmc/articles/PMC8723150/ /pubmed/34323947 http://dx.doi.org/10.1093/bioinformatics/btab561 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Wang, Shixiang Xiong, Yi Zhao, Longfei Gu, Kai Li, Yin Zhao, Fei Li, Jianfeng Wang, Mingjie Wang, Haitao Tao, Ziyu Wu, Tao Zheng, Yichao Li, Xuejun Liu, Xue-Song UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data |
title | UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data |
title_full | UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data |
title_fullStr | UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data |
title_full_unstemmed | UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data |
title_short | UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data |
title_sort | ucscxenashiny: an r/cran package for interactive analysis of ucsc xena data |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8723150/ https://www.ncbi.nlm.nih.gov/pubmed/34323947 http://dx.doi.org/10.1093/bioinformatics/btab561 |
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