zhangjunpeng411/miRspongeR: Identification and analysis of miRNA sponge regulation

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.

Getting started

Package details

AuthorJunpeng Zhang
Bioconductor views BiomedicalInformatics GeneExpression Microarray NetworkEnrichment RNASeq SingleCell Software Spatial Survival
MaintainerJunpeng Zhang <zhangjunpeng411@gmail.com>
URL <https://github.com/zhangjunpeng411/miRspongeR>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
zhangjunpeng411/miRspongeR documentation built on Sept. 28, 2022, 2:34 p.m.