ceRNAnetsim

DOI: 10.18129/B9.bioc.ceRNAnetsim    

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

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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 1.2.1
In Bioconductor since BioC 3.11 (R-4.0) (0.5 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_1.2.1.tar.gz
Windows Binary ceRNAnetsim_1.2.1.zip
macOS 10.13 (High Sierra) ceRNAnetsim_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/ceRNAnetsim
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ceRNAnetsim
Package Short Url https://bioconductor.org/packages/ceRNAnetsim/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive

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