miRspongeR

DOI: 10.18129/B9.bioc.miRspongeR  

Identification and analysis of miRNA sponge regulation

Bioconductor version: Release (3.16)

This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network.

Author: Junpeng Zhang

Maintainer: Junpeng Zhang <zhangjunpeng411 at gmail.com>

Installation

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

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

BiocManager::install("miRspongeR")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("miRspongeR")

 

HTML	R Script	Identification and analysis of miRNA sponge regulation
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, GeneExpression, Microarray, NetworkEnrichment, RNASeq, SingleCell, Software, Spatial, Survival
Version	2.2.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 years)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/zhangjunpeng411/miRspongeR/issues
Depends On Me
Imports Me	miRSM
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	miRspongeR_2.2.0.tar.gz
Windows Binary	miRspongeR_2.2.0.zip (64-bit only)
macOS Binary (x86_64)	miRspongeR_2.2.0.tgz
macOS Binary (arm64)	miRspongeR_2.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/miRspongeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/miRspongeR
Bioc Package Browser	https://code.bioconductor.org/browse/miRspongeR/
Package Short Url	https://bioconductor.org/packages/miRspongeR/
Package Downloads Report	Download Stats