{"id":20751301,"url":"https://github.com/cbg-ethz/clustnet","last_synced_at":"2026-03-02T10:31:35.605Z","repository":{"id":193303882,"uuid":"468686273","full_name":"cbg-ethz/clustNet","owner":"cbg-ethz","description":"Network-based clustering","archived":false,"fork":false,"pushed_at":"2024-02-15T08:40:38.000Z","size":18180,"stargazers_count":7,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-09T23:08:42.962Z","etag":null,"topics":["bayesian-network","bayesian-networks","clustering","dag","genomics","mixture-model","network-clustering"],"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/cbg-ethz.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","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}},"created_at":"2022-03-11T09:26:38.000Z","updated_at":"2024-12-31T15:28:41.000Z","dependencies_parsed_at":null,"dependency_job_id":"2bc63c7b-1a3a-44eb-97e4-eff7e398e3ee","html_url":"https://github.com/cbg-ethz/clustNet","commit_stats":null,"previous_names":["cbg-ethz/clustnet"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/cbg-ethz/clustNet","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2FclustNet","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2FclustNet/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2FclustNet/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2FclustNet/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cbg-ethz","download_url":"https://codeload.github.com/cbg-ethz/clustNet/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2FclustNet/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29998513,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-02T09:59:02.300Z","status":"ssl_error","status_checked_at":"2026-03-02T09:59:02.001Z","response_time":60,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["bayesian-network","bayesian-networks","clustering","dag","genomics","mixture-model","network-clustering"],"created_at":"2024-11-17T08:32:33.373Z","updated_at":"2026-03-02T10:31:35.560Z","avatar_url":"https://github.com/cbg-ethz.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"clustNet: Network-based clustering with covariate adjustment\n-----------\n\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n\n`clustNet` is an R package for network-based clustering of categorical data using a Bayesian network mixture model and optional covariate adjustment.\n\nInstallation\n-----------\n\nThe package requires `Rgraphviz` and `RBGL`, which can be installed from Bioconductor as follows:\n\n```{r eval=FALSE}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE)) install.packages(\"BiocManager\")\nBiocManager::install(c(\"Rgraphviz\", \"RBGL\"))\n```\n\nThe latest stable version of clustNet is available on CRAN and can be installed with\n\n```{r eval=FALSE}\ninstall.packages(\"clustNet\")\n```\nfrom within an R session. On a normal computer, this should take around 5-60 seconds, depending on how many of the required packages are already installed.\n\nBiocManager::install(\"remotes\")\n\nBeing hosted on GitHub, it is also possible to use the `install_github` tool from an R session to install the latest development version:\n\n```{r eval=FALSE}\nlibrary(\"devtools\")\ninstall_github(\"cbg-ethz/clustNet\")\n```\n\n`clustNet` requires R `\u003e= 3.5`.\n\n\nExample\n-------\n\n```{r eval=FALSE}\nlibrary(clustNet)\n\n# Simulate data\nk_clust \u003c- 3 # numer of clusters\nss \u003c- c(400, 500, 600) # samples in each cluster\nsimulation_data \u003c- sampleData(k_clust = k_clust, n_vars = 20, n_samples = ss)\nsampled_data \u003c- simulation_data$sampled_data\n\n# Network-based clustering\ncluster_results \u003c- get_clusters(sampled_data, k_clust = k_clust)\n\n# Load additional pacakges to visualize the networks\nlibrary(ggplot2)\nlibrary(ggraph)\nlibrary(igraph)\nlibrary(ggpubr)\n\n# Visualize networks\nplot_clusters(cluster_results)\n\n# Load additional pacakges to create a 2d dimensionality reduction\nlibrary(car)\nlibrary(ks)\nlibrary(graphics)\nlibrary(stats)\n\n# Plot a 2d dimensionality reduction\ndensity_plot(cluster_results)\n\n```\n\nOn a normal computer, the clustering should take around 2-4 minutes.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fclustnet","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcbg-ethz%2Fclustnet","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fclustnet/lists"}