{"id":15600894,"url":"https://github.com/karenxzr/multinep","last_synced_at":"2025-09-18T09:46:00.905Z","repository":{"id":68560681,"uuid":"471536150","full_name":"Karenxzr/MultiNEP","owner":"Karenxzr","description":"MultiNEP: a Multi-omics Network Enhancement framework for Prioritizing disease genes and metabolites simultanuously","archived":false,"fork":false,"pushed_at":"2023-06-09T17:32:15.000Z","size":8407,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-30T10:35:06.230Z","etag":null,"topics":["multi-omics","network-analysis","signal-prioritization"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Karenxzr.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2022-03-18T22:42:02.000Z","updated_at":"2023-05-24T12:37:36.000Z","dependencies_parsed_at":null,"dependency_job_id":"89e2017c-3394-42a5-8cd5-7a83c9d248b5","html_url":"https://github.com/Karenxzr/MultiNEP","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Karenxzr/MultiNEP","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Karenxzr%2FMultiNEP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Karenxzr%2FMultiNEP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Karenxzr%2FMultiNEP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Karenxzr%2FMultiNEP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Karenxzr","download_url":"https://codeload.github.com/Karenxzr/MultiNEP/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Karenxzr%2FMultiNEP/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":275746520,"owners_count":25521177,"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","status":"online","status_checked_at":"2025-09-18T02:00:09.552Z","response_time":77,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["multi-omics","network-analysis","signal-prioritization"],"created_at":"2024-10-03T02:07:20.465Z","updated_at":"2025-09-18T09:46:00.896Z","avatar_url":"https://github.com/Karenxzr.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MultiNEP: a Multi-omics Network Enhancement framework for Prioritizing disease genes and metabolites simultanuously\n\n\u003cimg width=\"898\" alt=\"image\" src=\"https://user-images.githubusercontent.com/27308407/206234973-b4c3a6b0-0bce-48a7-ac79-8bb2f74fbcbb.png\"\u003e\n\nMultiNEP is an improved analytical tool to prioritize disease-associated genes and metabolites simultanuously using multi-omics network with the ability to handle network imbalance. Multinep first reweight a general multi-omics network $S^0$ from database and a multi-omics similarity matrix $E$ based on disease profiles into $\\tilde{S^0}$ and $\\tilde{E}$ using weighting parameters $\\lambda_g$ and $\\lambda_m$. Then using reweighted $\\tilde{E}$ to enhance reweighted $\\tilde{S^0}$ into a disease-specific network $S_E$. At last, update initial disease-association gene and metabolite scores by diffusing on the enhanced and denoised multi-omics network $S_E$, and prioritize candidate disease-associated genes and metabolites simultanuously using updated disease-association gene and metabolite scores. \n\n## Installation\n\n- The R package of MultiNEP can be installed through:\u003cbr /\u003e\n`if (!requireNamespace(\"devtools\", quietly = TRUE))` \u003cbr /\u003e\n`install.packages(\"devtools\")`\u003cbr /\u003e\n`library(\"devtools\")`\u003cbr /\u003e\n`install_github(\"Karenxzr/MultiNEP\")`\n\n## Usage\n\nIt is quite simple to run MultiNEP through a wrapper function of `nep`. \nInput required:\n- General network `s0`: an $n \\times n$ matrix. With rownames and colnames being set as gene/metabolite names.\n- Disease similarity matrix `E`: an $n \\times n$ matrix. With rownames and colnames being set as gene/metabolite names. Note, all values in E should range from 0 - 1.\n- Initial disease association scores `signal`: a dataframe with the first column being feature names, the second column being initial association scores. Input p-values as default association scores.\n- Feature name list `feature_name_list`: a list with the first element containing all gene names and the second containing all metabolite names. \n\nYou can find sample input data within pacakge or in the `data` folder. See an application example as below:\n\n`library(MultiNEP)` \u003cbr /\u003e\n`results = nep(s0=s0,E=E,signals=signal,feature_name_list = feature_name_list, model='multinep')` \u003cbr /\u003e\n\nRun `results$vec` to get prioritized candidate disease-associated multi-omics features. If you want to get re-weighted and enhanced disease-specific multi-omics network $S_E$, run `results$enhanced_mat$unprocessed` or `results$enhanced_mat$processed` with `return_mat` argument set as TRUE.  \u003cbr /\u003e\n\nYou can also change parameters such as $\\lambda_g$ or $\\lambda_m$. Run `?nep` to find more details.\n\n## Reference\n- Zhuoran Xu, Luigi Marchionni, Shuang Wang, MultiNEP: a multi-omics network enhancement framework for prioritizing disease genes and metabolites simultaneously, Bioinformatics, Volume 39, Issue 6, June 2023, btad333, https://doi.org/10.1093/bioinformatics/btad333\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarenxzr%2Fmultinep","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkarenxzr%2Fmultinep","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarenxzr%2Fmultinep/lists"}