miRSM

DOI: 10.18129/B9.bioc.miRSM    

This is the development version of miRSM; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.10)

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 (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews BiomedicalInformatics, Clustering, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneTarget, Microarray, Software
Version 1.3.0
In Bioconductor since BioC 3.8 (R-3.5) (0.5 years)
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, dbscan, subspace, mclust, SOMbrero, ppclust, miRspongeR, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db
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_1.3.0.tar.gz
Windows Binary miRSM_1.3.0.zip
Mac OS X 10.11 (El Capitan) miRSM_1.3.0.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 http://bioconductor.org/packages/miRSM/
Package Downloads Report Download Stats

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