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 of ceRNAnetsim:

if (!requireNamespace("BiocManager", quietly = TRUE))


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


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