## ceRNAnetsim <!-- badges: start --> [](http://www.gnu.org/licenses/gpl-3.0) [](https://mybinder.org/v2/gh/selcenari/ceRNAnetsim/services?urlpath=rstudio) [](https://travis-ci.org/selcenari/ceRNAnetsim) [](https://codecov.io/gh/selcenari/ceRNAnetsim?branch=master) <!-- badges: end --> <p align="center"> <img width="500" height="300" src="https://media.giphy.com/media/l0ErNdz1w5vt3YdZm/giphy.gif"> </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](https://portal.gdc.cancer.gov/projects?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22projects.project_id%22%2C%22value%22%3A%5B%22TCGA-BRCA%22%5D%7D%7D%5D%7D) 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](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650559/) & [CLEAR-CLiP](https://www.nature.com/articles/ncomms9864) methods) - The remaining datasets are used as reproducible example of methods shown as [Mirtarbase example](https://selcenari.github.io/ceRNAnetsim/articles/mirtarbase_example.html) ## Vignettes The repository of ceRNAnetsim contents the vignettes that follow: - [What does ceRNAnetsim do?](https://selcenari.github.io/ceRNAnetsim/articles/basic_usage.html) - [How to calculate proper number of iterations for simulation of the network](https://selcenari.github.io/ceRNAnetsim/articles/convenient_iteration.html) - [How does the system do in a real-world network?](https://selcenari.github.io/ceRNAnetsim/articles/mirtarbase_example.html) - [Helper functions for users.](https://selcenari.github.io/ceRNAnetsim/articles/auxiliary_commands.html) Also see [package webpage](https://selcenari.github.io/ceRNAnetsim/) ## Issues Contact us for any issue or bug via: - [Issues](https://github.com/selcenari/ceRNAnetsim/issues) - [Alper Yilmaz](mailto:alperyilmaz@gmail.com) - [Selcen Ari](mailto:selcenarii@gmail.com)