miRspongeR
Identification and analysis of miRNA sponge regulation
Bioconductor version: Release (3.20)
This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network.
Author: Junpeng Zhang [aut, cre]
Maintainer: Junpeng Zhang <zjp at dali.edu.cn>
citation("miRspongeR")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("miRspongeR")
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("miRspongeR")| Identification and analysis of miRNA sponge regulation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, GeneExpression, Microarray, NetworkEnrichment, RNASeq, SingleCell, Software, Spatial, Survival |
| Version | 2.10.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.4.0) |
| Imports | corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/zhangjunpeng411/miRspongeR/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| 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 | miRspongeR_2.10.0.tar.gz |
| Windows Binary (x86_64) | miRspongeR_2.10.0.zip (64-bit only) |
| macOS Binary (x86_64) | miRspongeR_2.10.0.tgz |
| macOS Binary (arm64) | miRspongeR_2.9.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/miRspongeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/miRspongeR |
| Bioc Package Browser | https://code.bioconductor.org/browse/miRspongeR/ |
| Package Short Url | https://bioconductor.org/packages/miRspongeR/ |
| Package Downloads Report | Download Stats |