Jialab-UCR/GDCRNATools: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
Version 0.99.16

This is an easy-to-use package for downloading, organizing, and integrative analyzing RNA expression data in GDC with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer. Three databases of lncRNA-miRNA interactions including spongeScan, starBase, and miRcode, as well as three databases of mRNA-miRNA interactions including miRTarBase, starBase, and miRcode are incorporated into the package for ceRNAs network construction. limma, edgeR, and DESeq2 can be used to identify differentially expressed genes/miRNAs. Functional enrichment analyses including GO, KEGG, and DO can be performed based on the clusterProfiler and DO packages. Both univariate CoxPH and KM survival analyses of multiple genes can be implemented in the package. Besides some routine visualization functions such as volcano plot, bar plot, and KM plot, a few simply shiny apps are developed to facilitate visualization of results on a local webpage.

Getting started

Package details

AuthorRuidong Li, Han Qu, Shibo Wang, Julong Wei, Le Zhang, Renyuan Ma, Jianming Lu, Jianguo Zhu, Wei-De Zhong, Zhenyu Jia
Bioconductor views DifferentialExpression GO GeneExpression GeneRegulation GeneSetEnrichment GeneTarget KEGG Network NetworkEnrichment NetworkInference RNASeq Survival Visualization
MaintainerRuidong Li <[email protected]>, Han Qu <[email protected]>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
Jialab-UCR/GDCRNATools documentation built on Jan. 30, 2018, 7:37 p.m.