HFCAS OpenIR  > 中科院合肥智能机械研究所
CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization
Xu, Taosheng1; Thuc Duy Le2,3; Liu, Lin2; Su, Ning1; Wang, Rujing1; Sun, Bingyu1; Colaprico, Antonio4,5; Bontempi, Gianluca4,5; Li, Jiuyong2
2017-10-01
Source PublicationBIOINFORMATICS
Volume33Issue:19Pages:3131-3133
AbstractIdentifying 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.
SubtypeArticle
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine ; Technology ; Physical Sciences
Funding OrganizationAustralian Research Council(DP140103617) ; Australian Research Council(DP140103617) ; NHMRC(1123042) ; NHMRC(1123042) ; National Natural Science Foundation of China(31371340) ; National Natural Science Foundation of China(31371340) ; BridgeIRIS project - INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium ; BridgeIRIS project - INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium ; GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR(T100914F) ; GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR(T100914F) ; Australian Research Council(DP140103617) ; Australian Research Council(DP140103617) ; NHMRC(1123042) ; NHMRC(1123042) ; National Natural Science Foundation of China(31371340) ; National Natural Science Foundation of China(31371340) ; BridgeIRIS project - INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium ; BridgeIRIS project - INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium ; GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR(T100914F) ; GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR(T100914F)
DOI10.1093/bioinformatics/btx378
WOS KeywordDISCOVERY
Indexed BySCI
Language英语
Funding OrganizationAustralian Research Council(DP140103617) ; Australian Research Council(DP140103617) ; NHMRC(1123042) ; NHMRC(1123042) ; National Natural Science Foundation of China(31371340) ; National Natural Science Foundation of China(31371340) ; BridgeIRIS project - INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium ; BridgeIRIS project - INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium ; GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR(T100914F) ; GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR(T100914F) ; Australian Research Council(DP140103617) ; Australian Research Council(DP140103617) ; NHMRC(1123042) ; NHMRC(1123042) ; National Natural Science Foundation of China(31371340) ; National Natural Science Foundation of China(31371340) ; BridgeIRIS project - INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium ; BridgeIRIS project - INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium ; GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR(T100914F) ; GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR(T100914F)
WOS Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS SubjectBiochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS IDWOS:000411514100032
Citation statistics
Document Type期刊论文
Identifierhttp://ir.hfcas.ac.cn:8080/handle/334002/33721
Collection中科院合肥智能机械研究所
Affiliation1.Chinese Acad Sci, Hefei Inst Phys Sci, Inst Intelligent Machines, Hefei 230031, Anhui, Peoples R China
2.Univ South Australia, Sch Informat Technol & Math Sci, Adelaide, SA 5095, Australia
3.Univ South Australia, Ctr Canc Biol, Adelaide, SA 5000, Australia
4.ULB, Interuniv Inst Bioinformat Brussels IB2, B-1050 Brussels, Belgium
5.ULB, MLG, Dept Informat, B-1050 Brussels, Belgium
Recommended Citation
GB/T 7714
Xu, Taosheng,Thuc Duy Le,Liu, Lin,et al. CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization[J]. BIOINFORMATICS,2017,33(19):3131-3133.
APA Xu, Taosheng.,Thuc Duy Le.,Liu, Lin.,Su, Ning.,Wang, Rujing.,...&Li, Jiuyong.(2017).CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization.BIOINFORMATICS,33(19),3131-3133.
MLA Xu, Taosheng,et al."CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization".BIOINFORMATICS 33.19(2017):3131-3133.
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