{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T07:23:11Z","timestamp":1775028191153,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2017,6,12]],"date-time":"2017-06-12T00:00:00Z","timestamp":1497225600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP140103617"],"award-info":[{"award-number":["DP140103617"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["NHMRC"],"award-info":[{"award-number":["NHMRC"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["1123042"],"award-info":[{"award-number":["1123042"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31371340"],"award-info":[{"award-number":["31371340"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Identifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes, an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization. The input and output of each step in the framework are packaged in the same data format, making it convenience to compare different methods. The package is useful for inferring cancer subtypes from an input genomic dataset, comparing the predictions from different well-known methods and testing new subtype discovery methods, as shown with different application scenarios in the Supplementary Material.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The package is implemented in R and available under GPL-2 license from the Bioconductor website (http:\/\/bioconductor.org\/packages\/CancerSubtypes\/).<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx378","type":"journal-article","created":{"date-parts":[[2017,6,8]],"date-time":"2017-06-08T11:09:22Z","timestamp":1496920162000},"page":"3131-3133","source":"Crossref","is-referenced-by-count":211,"title":["CancerSubtypes: an R\/Bioconductor package for molecular cancer subtype identification, validation and visualization"],"prefix":"10.1093","volume":"33","author":[{"given":"Taosheng","family":"Xu","sequence":"first","affiliation":[{"name":"Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China"}]},{"given":"Thuc Duy","family":"Le","sequence":"additional","affiliation":[{"name":"School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, SA, Australia"},{"name":"Centre for Cancer Biology, University of South Australia, Adelaide, SA, Australia"}]},{"given":"Lin","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, SA, Australia"}]},{"given":"Ning","family":"Su","sequence":"additional","affiliation":[{"name":"Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China"}]},{"given":"Rujing","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China"}]},{"given":"Bingyu","family":"Sun","sequence":"additional","affiliation":[{"name":"Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China"}]},{"given":"Antonio","family":"Colaprico","sequence":"additional","affiliation":[{"name":"Interuniversity Institute of Bioinformatics in Brussels (IB)2, Universit\u00e9 Libre de Bruxelles (ULB), Brussels, Belgium"},{"name":"Machine Learning Group (MLG), Department d\u2019Informatique, Universit\u00e9 Libre de Bruxelles (ULB), Brussels, Belgium"}]},{"given":"Gianluca","family":"Bontempi","sequence":"additional","affiliation":[{"name":"Interuniversity Institute of Bioinformatics in Brussels (IB)2, Universit\u00e9 Libre de Bruxelles (ULB), Brussels, Belgium"},{"name":"Machine Learning Group (MLG), Department d\u2019Informatique, Universit\u00e9 Libre de Bruxelles (ULB), Brussels, Belgium"}]},{"given":"Jiuyong","family":"Li","sequence":"additional","affiliation":[{"name":"School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, SA, Australia"}]}],"member":"286","published-online":{"date-parts":[[2017,6,12]]},"reference":[{"key":"2023020206464058400_btx378-B1","doi-asserted-by":"crossref","first-page":"4164","DOI":"10.1073\/pnas.0308531101","article-title":"Metagenes and molecular pattern discovery using matrix factorization","volume":"101","author":"Brunet","year":"2004","journal-title":"Proc. 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