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miRSM

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

Inferring miRNA sponge modules in heterogeneous data


Bioconductor version: Development (3.19)

The package aims to identify miRNA sponge or ceRNA modules in heterogeneous data. It provides several functions to study miRNA sponge modules at single-sample and multi-sample levels, including popular methods for inferring gene modules (candidate miRNA sponge or ceRNA modules), and two functions to identify miRNA sponge modules at single-sample and multi-sample levels, as well as several functions to conduct modular analysis of miRNA sponge modules.

Author: Junpeng Zhang [aut, cre]

Maintainer: Junpeng Zhang <zjp at dali.edu.cn>

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

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("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")
miRSM: inferring miRNA sponge modules in heterogeneous data HTML R Script
Reference Manual PDF

Details

biocViews BiomedicalInformatics, Clustering, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneTarget, Microarray, Software
Version 1.99.8
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-3
Depends R (>= 3.5.0)
Imports WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE, MatrixCorrelation, energy
System Requirements
URL https://github.com/zhangjunpeng411/miRSM
Bug Reports https://github.com/zhangjunpeng411/miRSM/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package miRSM_1.99.8.tar.gz
Windows Binary miRSM_1.99.8.zip
macOS Binary (x86_64) miRSM_1.99.8.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/miRSM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/miRSM
Bioc Package Browser https://code.bioconductor.org/browse/miRSM/
Package Short Url https://bioconductor.org/packages/miRSM/
Package Downloads Report Download Stats