ceRNAnetsim

This is the development version of ceRNAnetsim; for the stable release version, see ceRNAnetsim.

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

Bioconductor version: Development (3.21)

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] (ORCID: ), Alper Yilmaz [aut] (ORCID: )

Maintainer: Selcen Ari Yuka <selcenarii at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GraphAndNetwork, Network, NetworkInference, Software, SystemsBiology, Transcriptomics
Version	1.19.0
In Bioconductor since	BioC 3.11 (R-4.0) (4.5 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

Suggests	knitr, png, rmarkdown, testthat, covr
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	ceRNAnetsim_1.19.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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