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miRspongeR

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

Identification and analysis of miRNA sponge regulation


Bioconductor version: Development (3.19)

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>

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

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

Details

biocViews BiomedicalInformatics, GeneExpression, Microarray, NetworkEnrichment, RNASeq, SingleCell, Software, Spatial, Survival
Version 2.7.0
In Bioconductor since BioC 3.9 (R-3.6) (5 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
System Requirements
URL
Bug Reports https://github.com/zhangjunpeng411/miRspongeR/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat
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 miRspongeR_2.7.0.tar.gz
Windows Binary miRspongeR_2.7.0.zip
macOS Binary (x86_64) miRspongeR_2.7.0.tgz
macOS Binary (arm64) miRspongeR_2.7.0.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