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## ceRNAnetsim <!-- badges: start --> [![License: GPL v3](]( [![Binder](]( [![Travis build status](]( [![Codecov test coverage](]( <!-- badges: end --> <p align="center"> <img width="500" height="300" src=""> </p> `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`: ```R 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](