miRSM

DOI: 10.18129/B9.bioc.miRSM    

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

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

Bioconductor version: Development (3.9)

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 a function to conduct functional analysis of miRNA sponge modules.

Author: Junpeng Zhang [aut, cre]

Maintainer: Junpeng Zhang <zhangjunpeng_411 at yahoo.com>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("miRSM", version = "3.9")

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 1.1.0
License GPL-3
Depends R (>= 3.5.0)
Imports WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, NMF, biclust, runibic, iBBiG, fabia, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, miRsponge, Rcpp, utils, SummarizedExperiment, GSEABase
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat, org.Hs.eg.db
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_1.1.0.tar.gz
Windows Binary miRSM_1.1.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)
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 http://bioconductor.org/packages/miRSM/
Package Downloads Report Download Stats

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