GDCRNATools
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
Bioconductor version: Release (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("GDCRNATools")):
Installation
To install this package, start R (version "4.4") 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
| Reference Manual | |
| NEWS | Text |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GO, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneTarget, ImmunoOncology, KEGG, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Survival, Visualization |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, testthat, prettydoc, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GDCRNATools_1.24.0.tar.gz |
| Windows Binary (x86_64) | GDCRNATools_1.24.0.zip (64-bit only) |
| macOS Binary (x86_64) | GDCRNATools_1.24.0.tgz |
| macOS Binary (arm64) | GDCRNATools_1.24.0.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/ |
| Package Downloads Report | Download Stats |