https://github.com/selcenari/cernanetsim
Simulation of interactions miRNA:Competing Targets
https://github.com/selcenari/cernanetsim
cerna mirna network-biology network-simulator r tcga tidygraph tidyverse
Last synced: about 2 months ago
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Simulation of interactions miRNA:Competing Targets
- Host: GitHub
- URL: https://github.com/selcenari/cernanetsim
- Owner: selcenari
- Created: 2019-03-15T09:47:04.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2024-02-08T11:57:14.000Z (over 1 year ago)
- Last Synced: 2025-04-13T12:14:03.451Z (about 2 months ago)
- Topics: cerna, mirna, network-biology, network-simulator, r, tcga, tidygraph, tidyverse
- Language: R
- Homepage:
- Size: 28.9 MB
- Stars: 5
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
## ceRNAnetsim
[](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)
`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:[email protected])
- [Selcen Ari](mailto:[email protected])