{"id":15292979,"url":"https://github.com/selcenari/cernanetsim","last_synced_at":"2025-06-25T18:06:52.714Z","repository":{"id":36403476,"uuid":"175792537","full_name":"selcenari/ceRNAnetsim","owner":"selcenari","description":"Simulation of interactions miRNA:Competing Targets","archived":false,"fork":false,"pushed_at":"2024-02-08T11:57:14.000Z","size":30296,"stargazers_count":5,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-06-16T14:59:35.127Z","etag":null,"topics":["cerna","mirna","network-biology","network-simulator","r","tcga","tidygraph","tidyverse"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/selcenari.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2019-03-15T09:47:04.000Z","updated_at":"2025-04-10T14:42:39.000Z","dependencies_parsed_at":"2023-12-18T09:47:30.160Z","dependency_job_id":"bef5a999-8b4b-4981-95b6-c324b473e5d2","html_url":"https://github.com/selcenari/ceRNAnetsim","commit_stats":{"total_commits":412,"total_committers":4,"mean_commits":103.0,"dds":"0.40533980582524276","last_synced_commit":"9640236cd76d290feac762c9ae7872adf0f63986"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/selcenari/ceRNAnetsim","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/selcenari%2FceRNAnetsim","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/selcenari%2FceRNAnetsim/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/selcenari%2FceRNAnetsim/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/selcenari%2FceRNAnetsim/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/selcenari","download_url":"https://codeload.github.com/selcenari/ceRNAnetsim/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/selcenari%2FceRNAnetsim/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261927549,"owners_count":23231375,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cerna","mirna","network-biology","network-simulator","r","tcga","tidygraph","tidyverse"],"created_at":"2024-09-30T16:36:47.906Z","updated_at":"2025-06-25T18:06:52.245Z","avatar_url":"https://github.com/selcenari.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n## ceRNAnetsim\n\n\u003c!-- badges: start --\u003e\n[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/selcenari/ceRNAnetsim/services?urlpath=rstudio) \n[![Travis build status](https://travis-ci.org/selcenari/ceRNAnetsim.svg?branch=master)](https://travis-ci.org/selcenari/ceRNAnetsim)\n[![Codecov test coverage](https://codecov.io/gh/selcenari/ceRNAnetsim/branch/master/graph/badge.svg)](https://codecov.io/gh/selcenari/ceRNAnetsim?branch=master)\n\u003c!-- badges: end --\u003e\n\n\n\u003cp align=\"center\"\u003e\n  \u003cimg width=\"500\" height=\"300\" src=\"https://media.giphy.com/media/l0ErNdz1w5vt3YdZm/giphy.gif\"\u003e\n\u003c/p\u003e\n\n`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.\n\n\n## Installation\n\nInstallation of `ceRNAnetsim`:\n\n```R\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"ceRNAnetsim\")\n\nlibrary(ceRNAnetsim)\n\n```\n\n## Example\n\n```\ndata(\"minsamp\")\n\nminsamp\n\npriming_graph(minsamp, \n                competing_count = Competing_expression, \n                miRNA_count = miRNA_expression)\n\n```\n\n\n## Local Files\n\nThe `ceRNAnetsim` provides various datasets for experimenting with package functions. These are:\n\n- *minsamp* : the minimum sample consists of 2 miRNAs and 6 genes which are targeted by them. *new_counts* is a helper dataset for *minsamp*.\n- *midsamp* : middle-sized sample is a network of 4 miRNAs and 20 competing target genes.\n- *huge_example* : this dataset is comprised of a large network which incorporates three datasets: \n  - 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 \n  - miRNA expression of a breast cancer patient (from TCGA)\n  - and the miRNA:target dataset gathered from two different high-throughput experimental studies. ([CLASH](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650559/) \u0026 [CLEAR-CLiP](https://www.nature.com/articles/ncomms9864) methods)\n- The remaining datasets are used as reproducible example of methods shown as [Mirtarbase example](https://selcenari.github.io/ceRNAnetsim/articles/mirtarbase_example.html)\n\n## Vignettes\n\nThe repository of ceRNAnetsim contents the vignettes that follow:\n\n- [What does ceRNAnetsim do?](https://selcenari.github.io/ceRNAnetsim/articles/basic_usage.html)\n- [How to calculate proper number of iterations for simulation of the network](https://selcenari.github.io/ceRNAnetsim/articles/convenient_iteration.html)\n- [How does the system do in a real-world network?](https://selcenari.github.io/ceRNAnetsim/articles/mirtarbase_example.html)\n- [Helper functions for users.](https://selcenari.github.io/ceRNAnetsim/articles/auxiliary_commands.html)\n\nAlso see [package webpage](https://selcenari.github.io/ceRNAnetsim/)\n\n\n## Issues\n\nContact us for any issue or bug via:\n\n- [Issues](https://github.com/selcenari/ceRNAnetsim/issues)\n- [Alper Yilmaz](mailto:alperyilmaz@gmail.com)\n- [Selcen Ari](mailto:selcenarii@gmail.com)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fselcenari%2Fcernanetsim","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fselcenari%2Fcernanetsim","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fselcenari%2Fcernanetsim/lists"}