ceRNAnetsim

ceRNAnetsim helps to understanding complex miRNA:target interactions with the network based approach. It utilizes the amounts of miRNAs and their targets and interaction parameters optionally.

Installation

Installation of ceRNAnetsim:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ceRNAnetsim")

library(ceRNAnetsim)

Example

data("minsamp")

minsamp

priming_graph(minsamp, 
                competing_count = Competing_expression, 
                miRNA_count = miRNA_expression)

Local Files

The ceRNAnetsim provides various datasets for experimenting with package functions. These are:

• minsamp : the minimum sample consists of 2 miRNAs and 6 genes which are targeted by them. new_counts is a helper dataset for minsamp.
• midsamp : middle-sized sample is a network of 4 miRNAs and 20 competing target genes.
• huge_example : this dataset is comprised of a large network which incorporates three datasets:
  • gene expression levels (RNA-Seq) retrieved from TCGA-BRCA breast cancer
  • miRNA expression of a breast cancer patient (from TCGA)
  • and the miRNA:target dataset gathered from two different high-throughput experimental studies. (CLASH & CLEAR-CLiP methods)
• The remaining datasets are used as reproducible example of methods shown as Mirtarbase example

Vignettes

The repository of ceRNAnetsim contents the vignettes that follow:

• What does ceRNAnetsim do?
• How to calculate proper number of iterations for simulation of the network
• How does the system do in a real-world network?
• Helper functions for users.

Also see package webpage

Issues

Contact us for any issue or bug via:

• Issues
• Alper Yilmaz
• Selcen Ari