miRspongeR
Identification and analysis of miRNA sponge regulation
Bioconductor version: 3.24 · Package version: 2.17.4
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("miRspongeR")Details
| Maintainer | Junpeng Zhang <zjp@dali.edu.cn> |
| Author | Junpeng Zhang [aut, cre] |
| License | GPL-3 |
| URL | <https://github.com/zhangjunpeng411/miRspongeR> |
| Bug Reports | https://github.com/zhangjunpeng411/miRspongeR/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BiomedicalInformatics, GeneExpression, Microarray, NetworkEnrichment, RNASeq, SingleCell, Software, Spatial, Survival |
| Package Short Url | https://bioconductor.org/packages/miRspongeR/ |
Citation
From within R, enter citation("miRspongeR"):
Junpeng Zhang. miRspongeR: Identification and analysis of miRNA sponge regulation. doi:10.18129/B9.bioc.miRspongeR, R package version 2.17.4, https://bioconductor.org/packages/miRspongeR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | miRspongeR_2.17.4.tar.gz |
| Windows binary (x86_64) | miRspongeR_2.17.4.zip |
| macOS binary (arm64) | miRspongeR_2.17.4.tgz |
| macOS binary (x86_64) | miRspongeR_2.17.4.tgz |
Dependencies
Depends: R (>= 4.4.0)
Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, utils, Rcpp, RColorBrewer, grid, org.Hs.eg.db, foreach, doParallel