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GDCRNATools

This is the development version of GDCRNATools; for the stable release version, see GDCRNATools.

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


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("GDCRNATools")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("GDCRNATools")

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

Documentation

Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, GO, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneTarget, ImmunoOncology, KEGG, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Survival, Visualization
Version 1.23.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
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Suggests knitr, testthat, prettydoc, rmarkdown
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Package Archives

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

Source Package GDCRNATools_1.23.0.tar.gz
Windows Binary GDCRNATools_1.23.0.zip (64-bit only)
macOS Binary (x86_64) GDCRNATools_1.23.0.tgz
macOS Binary (arm64) GDCRNATools_1.23.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GDCRNATools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GDCRNATools
Bioc Package Browser https://code.bioconductor.org/browse/GDCRNATools/
Package Short Url https://bioconductor.org/packages/GDCRNATools/
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