miRSM

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8

Inferring miRNA sponge modules in heterogeneous data

Bioconductor version: Development (3.24)

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")):

Junpeng Zhang. miRSM: Inferring miRNA sponge modules in heterogeneous data. doi:10.18129/B9.bioc.miRSM, R package version 2.9.3, https://bioconductor.org/packages/miRSM.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, Clustering, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneTarget, Microarray, Software
Version	2.9.3
In Bioconductor since	BioC 3.8 (R-3.5) (8 years)
License	GPL-3
Depends	R (>= 4.4.0)
Imports	WGCNA, flashClust, dynamicTreeCut, GFA, igraph, RColorBrewer, grid, MCL, fabia, NMF, BicARE, isa2, methods, rJava, Biobase, PMA, stats, dbscan, 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

Suggests	BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	miRSM_2.9.3.tar.gz
Windows Binary (x86_64)	miRSM_2.9.3.zip
macOS Binary (big-sur-x86_64)	miRSM_2.9.3.tgz
macOS Binary (sonoma-arm64)	miRSM_2.9.3.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