{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T07:30:06Z","timestamp":1785310206097,"version":"3.55.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2018,3,2]],"date-time":"2018-03-02T00:00:00Z","timestamp":1519948800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Faculty Start-up Fund"},{"name":"UC Aca-demic Senate Regents Faculty Fellowship"},{"name":"National Key Basic Research Program of China","award":["2015CB553706"],"award-info":[{"award-number":["2015CB553706"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"crossref","award":["2017PY023"],"award-info":[{"award-number":["2017PY023"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Projects of Guizhou Province","award":["QKHW-G [2014]7004"],"award-info":[{"award-number":["QKHW-G [2014]7004"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81571427"],"award-info":[{"award-number":["81571427"]}],"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":["81641102"],"award-info":[{"award-number":["81641102"]}],"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":["81660426"],"award-info":[{"award-number":["81660426"]}],"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":["81360119"],"award-info":[{"award-number":["81360119"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The large-scale multidimensional omics data in the Genomic Data Commons (GDC) provides opportunities to investigate the crosstalk among different RNA species and their regulatory mechanisms in cancers. Easy-to-use bioinformatics pipelines are needed to facilitate such studies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed a user-friendly R\/Bioconductor package, named GDCRNATools, for downloading, organizing and analyzing RNA data in GDC with an emphasis on deciphering the lncRNA-mRNA related competing endogenous RNAs regulatory network in cancers. Many widely used bioinformatics tools and databases are utilized in our package. Users can easily pack preferred downstream analysis pipelines or integrate their own pipelines into the workflow. Interactive shiny web apps built in GDCRNATools greatly improve visualization of results from the analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>GDCRNATools is an R\/Bioconductor package that is freely available at Bioconductor (http:\/\/bioconductor.org\/packages\/devel\/bioc\/html\/GDCRNATools.html). Detailed instructions, manual and example code are also available in Github (https:\/\/github.com\/Jialab-UCR\/GDCRNATools).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty124","type":"journal-article","created":{"date-parts":[[2018,2,28]],"date-time":"2018-02-28T23:11:38Z","timestamp":1519859498000},"page":"2515-2517","source":"Crossref","is-referenced-by-count":157,"title":["<i>GDCRNATools<\/i>\n                    : an R\/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC"],"prefix":"10.1093","volume":"34","author":[{"given":"Ruidong","family":"Li","sequence":"first","affiliation":[{"name":"Department of Botany and Plant Sciences"},{"name":"Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Qu","sequence":"additional","affiliation":[{"name":"Department of Botany and Plant 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USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianming","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Botany and Plant Sciences"},{"name":"Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianguo","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei-De","family":"Zhong","sequence":"additional","affiliation":[{"name":"Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenyu","family":"Jia","sequence":"additional","affiliation":[{"name":"Department of Botany and Plant Sciences"},{"name":"Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,3,2]]},"reference":[{"key":"2023012713020054700_bty124-B1","doi-asserted-by":"crossref","first-page":"D296","DOI":"10.1093\/nar\/gkx1067","article-title":"miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions","volume":"46","author":"Chou","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023012713020054700_bty124-B2","doi-asserted-by":"crossref","first-page":"e71","DOI":"10.1093\/nar\/gkv1507","article-title":"TCGAbiolinks: an R\/Bioconductor package for integrative analysis of TCGA 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