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ceRNAnetsim

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


Bioconductor version: Release (3.18)

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 gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ceRNAnetsim")

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("ceRNAnetsim")
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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GraphAndNetwork, Network, NetworkInference, Software, SystemsBiology, Transcriptomics
Version 1.14.1
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL (>= 3.0)
Depends R (>= 4.0.0), dplyr, tidygraph
Imports furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats
System Requirements
URL https://github.com/selcenari/ceRNAnetsim
Bug Reports https://github.com/selcenari/ceRNAnetsim/issues
See More
Suggests knitr, png, rmarkdown, testthat, covr
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ceRNAnetsim_1.14.1.tar.gz
Windows Binary ceRNAnetsim_1.14.1.zip
macOS Binary (x86_64) ceRNAnetsim_1.14.1.tgz
macOS Binary (arm64) ceRNAnetsim_1.14.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/ceRNAnetsim
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ceRNAnetsim
Bioc Package Browser https://code.bioconductor.org/browse/ceRNAnetsim/
Package Short Url https://bioconductor.org/packages/ceRNAnetsim/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive