Facilitating integrative and personalized oncology omics analysis with UCSCXenaShiny
The continuous generation of multi-omics and phenotype data is propelling advancements in precision oncology. UCSCXenaShiny was developed as an interactive tool for exploring thousands of cancer datasets available on UCSC Xena. However, its capacity for comprehensive and personalized pan-cancer data analysis is being challenged by the growing demands. Here, we introduce UCSCXenaShiny v2, a milestone update through a variety of improvements. Firstly, by integrating multidimensional data and implementing adaptable sample settings, we create a suite of robust TPC (TCGA, PCAWG, CCLE) analysis pipelines. These pipelines empower users to conduct in-depth analyses of correlation, comparison, and survival in three modes: Individual, Pan-cancer and Batch screen. Additionally, the tool includes download interfaces that enable users to access diverse data and outcomes, several features also facilitate the joint analysis of drug sensitivity and multi-omics of cancer cell lines. UCSCXenaShiny v2 is an open-source R package and a web application, freely accessible at https://github.com/openbiox/UCSCXenaShiny .
Authors
- Sujun Chen (ORCID: https://orcid.org/0000-0002-1941-3951)
- Yi Xiong (ORCID: https://orcid.org/0000-0002-4370-9824)
- Shensuo Li (ORCID: https://orcid.org/0009-0006-3229-3700)
- Yuzhong Peng (ORCID: https://orcid.org/0000-0001-8011-6668)
- Peng Luo (ORCID: https://orcid.org/0000-0002-8215-2045)
- Yanru Cui (ORCID: https://orcid.org/0000-0002-2838-3491)
- Qi Zhao (ORCID: https://orcid.org/0000-0002-8683-6145)
- Fei Zhao (ORCID: https://orcid.org/0000-0002-9087-5243)
- Shixiang Wang (ORCID: https://orcid.org/0000-0001-9855-7357)
- Jian‐Guo Zhou (ORCID: https://orcid.org/0000-0002-5021-3739)
- Haitao Wang (ORCID: https://orcid.org/0000-0001-6910-974X)
- Jianfeng Li (ORCID: https://orcid.org/0000-0003-2349-208X)
- Yankun Zhao
- Minjun Chen (ORCID: https://orcid.org/0009-0001-7755-2466)
Institutions
- Macau University of Science and Technology (MO)
- Central South University (CN)
- Sun Yat-sen University (CN)
- Friedrich-Alexander-Universität Erlangen-Nürnberg (DE)
- Zunyi Medical University (CN)
- University of Macau (MO)
- Cornell University (US)
- Sichuan University (CN)
- Universitätsklinikum Erlangen (DE)
- West China Hospital of Sichuan University (CN)
- Zhujiang Hospital (CN)
- Sun Yat-sen University Cancer Center (CN)
- Shanghai Institute of Hematology (CN)
- Center for Cancer Research (US)
- University of Chinese Academy of Sciences (CN)
- Southern Medical University (CN)
Publication Details
- Journal
- Communications Biology
- Published
- 2024-09-28
- DOI
- https://doi.org/10.1038/s42003-024-06891-2
- Citations
- 10
- Primary Topic
- Bioinformatics and Genomic Networks
- Type
- article
- Field-Weighted Citation Impact
- 2.34
Funders
- National Natural Science Foundation of China
- Central South University
- China Postdoctoral Science Foundation
- Natural Science Foundation of Guizhou Province
- Department of Education of Guizhou Province
- Xiangya Hospital, Central South University
- Basic and Applied Basic Research Foundation of Guangdong Province