{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T23:47:30Z","timestamp":1782949650584,"version":"3.54.5"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,7,29]],"date-time":"2021-07-29T00:00:00Z","timestamp":1627516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771373"],"award-info":[{"award-number":["31771373"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81472594"],"award-info":[{"award-number":["81472594"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81770781"],"award-info":[{"award-number":["81770781"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Shanghai Science and Technology Commission","doi-asserted-by":"publisher","award":["21ZR1442400"],"award-info":[{"award-number":["21ZR1442400"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012600","name":"ShanghaiTech University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012600","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab561","type":"journal-article","created":{"date-parts":[[2021,7,28]],"date-time":"2021-07-28T07:13:43Z","timestamp":1627456423000},"page":"527-529","source":"Crossref","is-referenced-by-count":135,"title":["UCSCXenaShiny: an R\/CRAN package for interactive analysis of UCSC Xena data"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9855-7357","authenticated-orcid":false,"given":"Shixiang","family":"Wang","sequence":"first","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , 201203 Shanghai, China"},{"name":"Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , 200031 Shanghai, China"},{"name":"University of Chinese Academy of Sciences , 100049 Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Xiong","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Xiangya Hospital, Central South University , 410008 Changsha, China"},{"name":"Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University , 410008 Changsha, China"},{"name":"Xiangya School of Medicine, Central South University , 410013 Changsha, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longfei","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Sciences, Zhengzhou University , 450001 Zhengzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Gu","sequence":"additional","affiliation":[{"name":"Roche Diagnostics (Shanghai) Limited , 201107 Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Thoracic Surgery, Zhongshan Hospital, Fudan University , 200032 Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fei","family":"Zhao","sequence":"additional","affiliation":[{"name":"University of Chinese Academy of Sciences , 100049 Beijing, China"},{"name":"CAS Center for Excellence in Molecular Plant Sciences , 200032 Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianfeng","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University, School of Medicine , 200025 Shanghai, China"},{"name":"School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 200240 Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingjie","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University, School of Medicine , 200025 Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haitao","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, 999087 Macau SAR, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyu","family":"Tao","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , 201203 Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , 201203 Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yichao","family":"Zheng","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Sciences, Zhengzhou University , 450001 Zhengzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuejun","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Xiangya Hospital, Central South University , 410008 Changsha, China"},{"name":"Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University , 410008 Changsha, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7736-0077","authenticated-orcid":false,"given":"Xue-Song","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , 201203 Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,7,29]]},"reference":[{"key":"2023020108411443500_btab561-B1","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1126\/science.1262110","article-title":"The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans","volume":"348","author":"Ardlie","year":"2015","journal-title":"Science"},{"key":"2023020108411443500_btab561-B2","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug 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Open Source Softw"},{"key":"2023020108411443500_btab561-B12","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/ng.2764","article-title":"The Cancer Genome Atlas Pan-Cancer analysis project","volume":"45","author":"Weinstein","year":"2013","journal-title":"Nat. Genet"},{"key":"2023020108411443500_btab561-B13","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/s41587-019-0055-9","article-title":"The International Cancer Genome Consortium Data Portal","volume":"37","author":"Zhang","year":"2019","journal-title":"Nat. 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