miRSM

DOI: 10.18129/B9.bioc.miRSM    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see miRSM.

Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information

Bioconductor version: 3.11

The package aims to identify miRNA sponge modules by integrating expression data and miRNA-target binding information. It provides several functions to study miRNA sponge modules, including popular methods for inferring gene modules (candidate miRNA sponge modules), and a function to identify miRNA sponge modules, as well as several functions to conduct modular analysis of miRNA sponge modules.

Author: Junpeng Zhang [aut, cre]

Maintainer: Junpeng Zhang <zhangjunpeng_411 at yahoo.com>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("miRSM")

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("miRSM")

 

HTML	R Script	miRSM: inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, Clustering, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneTarget, Microarray, Software
Version	1.6.4
In Bioconductor since	BioC 3.8 (R-3.5) (2 years)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, NMF, biclust, iBBiG, fabia, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, miRspongeR, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, MatrixCorrelation, energy
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/zhangjunpeng411/miRSM
BugReports	https://github.com/zhangjunpeng411/miRSM/issues
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	miRSM_1.6.4.tar.gz
Windows Binary	miRSM_1.6.4.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	miRSM_1.6.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/miRSM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/miRSM
Package Short Url	https://bioconductor.org/packages/miRSM/
Package Downloads Report	Download Stats