GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC

被引：154

作者：

Li, Ruidong ^{[1
,2
]}

Qu, Han ^{[1
]}

Wang, Shibo ^{[1
]}

Wei, Julong ^{[1
,3
]}

Zhang, Le ^{[1
,2
]}

Ma, Renyuan ^{[1
,4
]}

Lu, Jianming ^{[1
,5
]}

Zhu, Jianguo ^{[6
]}

Zhong, Wei-De ^{[5
]}

Jia, Zhenyu ^{[1
,2
]}

机构：

[1] Univ Calif Riverside, Dept Bot & Plant Sci, Riverside, CA 92521 USA

[2] Univ Calif Riverside, Genet Gen & Bioinformat Program, Riverside, CA 92521 USA

[3] Nanjing Agr Univ, Coll Anim Sci & Technol, Nanjing 210095, Jiangsu, Peoples R China

[4] Bowdoin Coll, Dept Math, Brunswick, ME 04011 USA

[5] South China Univ Technol, Guangzhou Peoples Hosp 1, Affiliated Hosp 2, Dept Urol,Guangdong Key Lab Clin Mol Med & Diagno, Guangzhou 510180, Guangdong, Peoples R China

[6] Guizhou Prov Peoples Hosp, Dept Urol, Guiyang 550002, Guizhou, Peoples R China

来源：

BIOINFORMATICS | 2018年 / 34卷 / 14期

基金：

中国国家自然科学基金;

关键词：

D O I：

10.1093/bioinformatics/bty124

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: 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. Results: 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.

引用

页码：2515 / 2517

页数：3

共 15 条

[11] limma powers differential expression analyses for RNA-sequencing and microarray studies [J].

Ritchie, Matthew E. ;

Phipson, Belinda ;

Wu, Di ;

Hu, Yifang ;

Law, Charity W. ;

Shi, Wei ;

Smyth, Gordon K. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (07) :e47

[12] edgeR: a Bioconductor package for differential expression analysis of digital gene expression data [J].

Robinson, Mark D. ;

McCarthy, Davis J. ;

Smyth, Gordon K. .

BIOINFORMATICS, 2010, 26 (01) :139-140

[13] DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis [J].

Yu, Guangchuang ;

Wang, Li-Gen ;

Yan, Guang-Rong ;

He, Qing-Yu .

BIOINFORMATICS, 2015, 31 (04) :608-609

[14] clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters [J].

Yu, Guangchuang ;

Wang, Li-Gen ;

Han, Yanyan ;

He, Qing-Yu .

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 2012, 16 (05) :284-287

[15] TCGA-Assembler: open-source software for retrieving and processing TCGA data [J].

Zhu, Yitan ;

Qiu, Peng ;

Ji, Yuan .

NATURE METHODS, 2014, 11 (06) :599-600

← 1 2 →