GDCRNATools

DOI: 10.18129/B9.bioc.GDCRNATools    

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

Bioconductor version: Release (3.15)

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.

Author: Ruidong Li, Han Qu, Shibo Wang, Julong Wei, Le Zhang, Renyuan Ma, Jianming Lu, Jianguo Zhu, Wei-De Zhong, Zhenyu Jia

Maintainer: Ruidong Li <rli012 at ucr.edu>, Han Qu <hqu002 at ucr.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GDCRNATools")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GO, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneTarget, ImmunoOncology, KEGG, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Survival, Visualization
Version	1.16.6
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel
LinkingTo
Suggests	knitr, testthat, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GDCRNATools_1.16.6.tar.gz
Windows Binary	GDCRNATools_1.16.6.zip
macOS Binary (x86_64)	GDCRNATools_1.16.6.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GDCRNATools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GDCRNATools
Package Short Url	https://bioconductor.org/packages/GDCRNATools/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive