{"id":24529140,"url":"https://github.com/saezlab/phonemes","last_synced_at":"2025-04-14T17:11:01.000Z","repository":{"id":36056392,"uuid":"40354881","full_name":"saezlab/PHONEMeS","owner":"saezlab","description":" PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is an R package   to model signalling networks based on untargeted phosphoproteomics","archived":false,"fork":false,"pushed_at":"2024-04-29T13:42:26.000Z","size":197525,"stargazers_count":7,"open_issues_count":0,"forks_count":5,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-03-28T05:51:02.570Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://saezlab.github.io/PHONEMeS","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/saezlab.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":"2015-08-07T10:20:45.000Z","updated_at":"2024-04-29T13:42:30.000Z","dependencies_parsed_at":"2025-01-22T07:35:02.884Z","dependency_job_id":"710b34c2-1f27-465d-bd56-95834f8b4502","html_url":"https://github.com/saezlab/PHONEMeS","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FPHONEMeS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FPHONEMeS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FPHONEMeS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FPHONEMeS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/PHONEMeS/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248923764,"owners_count":21183954,"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":[],"created_at":"2025-01-22T07:34:57.358Z","updated_at":"2025-04-14T17:11:00.968Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PHONEMeS \u003cimg src=\"inst/figures/logo.png\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n\u003c!-- badges: end --\u003e\n\n## Overview\n\n`PHONEMeS` (**PHO**sphorylation **NE**tworks for **M**ass **S**pectrometry) is a method to model signalling networks based on untargeted phosphoproteomics mass spectrometry data and kinase/phosphatase-substrate interactions. \nIt is an extension of the Causal Reasoning tool `CARNIVAL` and focuses on identifying deregulated\nsignaling pathways by linking deregulated phosphorylation sites towards up-stream kinases. Additionally,\nit provides prior knowledge networks of kinase-substrate and protein-protein interactions extracted\nfrom `OmnipathR`.\n\nFor more information about this package, please check the following links:\n\n- [PHONEMeS vignette](https://github.com/saezlab/PHONEMeS/blob/master/vignettes/PHONEMeS.Rmd) (currently in development)\n- [PHONEMeS tutorial](https://github.com/saezlab/PHONEMeS/blob/master/vignettes/tutorial.md)\n\n\n## Installation\n\nTo install `PHONEMeS` please run:\n```\ndevtools::install_github('saezlab/PHONEMeS')\n```\n### Prerequisites\n\n`PHONEMeS` requires the interactive version of IBM Cplex or CBC-COIN solver as the network \noptimiser. The IBM ILOG Cplex is freely available through Academic Initiative [here](https://www.ibm.com/products/ilog-cplex-optimization-studio). The [CBC](https://projects.coin-or.org/Cbc) solver is open source and freely available\nfor any user. Alternatively for smaller cases, users can rely on the freely available \n[lpSolve R-package](https://cran.r-project.org/web/packages/lpSolve/index.html). \n\n\n## Prior versions\n\nThe code for the original PHONEMeS package (PHONEMeS v1.0.0) as described in Terfve et al. 2015 can be found in the releases.\nFor a guide how to run a PHONEMeS analysis using PHONEMeS v1.0.0, please refer to the [documentation](https://saezlab.github.io/PHONEMeS).\n\n\n## Citation\n\n[Terfve et al.](http://www.nature.com/articles/ncomms9033):\n\n\u003e Terfve, C. D. A., Wilkes, E. H., Casado, P., Cutillas, P. R., and Saez-Rodriguez, J. (2015). Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data. *Nature Communications*, 6:8033.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fphonemes","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fphonemes","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fphonemes/lists"}