miRSM
This package is for version 3.8 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: 3.8
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("miRSM")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("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")| miRSM: inferring miRNA sponge modules by integrating expression data and miRNA-target binding information | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, Clustering, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneTarget, Microarray, Software |
| Version | 1.0.0 |
| 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, NMF, biclust, runibic, iBBiG, fabia, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, miRsponge, Rcpp, utils, SummarizedExperiment, GSEABase |
| System Requirements | |
| URL | https://github.com/zhangjunpeng411/miRSM |
| Bug Reports | https://github.com/zhangjunpeng411/miRSM/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, org.Hs.eg.db |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | miRSM_1.0.0.tar.gz |
| Windows Binary | miRSM_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | miRSM_1.0.0.tgz |
| 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 |
| Old Source Packages for BioC 3.8 | Source Archive |