DOI: 10.18129/B9.bioc.ceRNAnetsim  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ceRNAnetsim.

Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

Bioconductor version: 3.16

This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables.

Author: Selcen Ari Yuka [aut, cre] , Alper Yilmaz [aut]

Maintainer: Selcen Ari Yuka <selcenarii at>

Citation (from within R, enter citation("ceRNAnetsim")):


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HTML R Script A Suggestion: How to Find the Appropriate Iteration for Simulation
HTML R Script An TCGA dataset application
HTML R Script auxiliary_commands
HTML R Script basic_usage
PDF   Reference Manual
Text   NEWS


biocViews GraphAndNetwork, Network, NetworkInference, Software, SystemsBiology, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License GPL (>= 3.0)
Depends R (>= 4.0.0), dplyr, tidygraph
Imports furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats
Suggests knitr, png, rmarkdown, testthat, covr
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