ceRNAnetsim

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 gmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

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
LinkingTo
Suggests	knitr, png, rmarkdown, testthat, covr
SystemRequirements
Enhances
URL	https://github.com/selcenari/ceRNAnetsim
BugReports	https://github.com/selcenari/ceRNAnetsim/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ceRNAnetsim_1.10.0.tar.gz
Windows Binary	ceRNAnetsim_1.10.0.zip
macOS Binary (x86_64)	ceRNAnetsim_1.10.0.tgz
macOS Binary (arm64)	ceRNAnetsim_1.10.0.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