miRsponge

DOI: 10.18129/B9.bioc.miRsponge    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see miRsponge (renamed to miRspongeR) .

Identification and analysis of miRNA sponge interaction networks and modules

Bioconductor version: 3.9

The name of the miRsponge package has been changed into "miRspongeR". Future updates will be seen in the miRspongeR package (http://bioconductor.org/packages/miRspongeR/). This package provides several functions to study miRNA sponge (also called ceRNA or miRNA decoy), including popular methods for identifying miRNA sponge interactions, and the 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 modules, and conduct survival analysis of modules.

Author: Junpeng Zhang

Maintainer: Junpeng Zhang <zhangjunpeng_411 at yahoo.com>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("miRsponge")

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("miRsponge")

 

HTML	R Script	miRsponge: identification and analysis of miRNA sponge interaction networks and modules
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, GeneExpression, Microarray, NetworkEnrichment, Software, Survival
Version	1.10.0
In Bioconductor since	BioC 3.6 (R-3.4) (2 years)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	corpcor, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, varhandle, linkcomm, utils, Rcpp, org.Hs.eg.db
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
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	miRsponge_1.10.0.tar.gz
Windows Binary	miRsponge_1.10.0.zip
Mac OS X 10.11 (El Capitan)	miRsponge_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/miRsponge
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/miRsponge
Package Short Url	https://bioconductor.org/packages/miRsponge/
Package Downloads Report	Download Stats