{"id":21699525,"url":"https://github.com/saezlab/OmnipathR","last_synced_at":"2025-07-18T10:31:42.770Z","repository":{"id":40486288,"uuid":"156886914","full_name":"saezlab/OmnipathR","owner":"saezlab","description":"R client for the OmniPath web service","archived":false,"fork":false,"pushed_at":"2024-11-18T16:56:04.000Z","size":34666,"stargazers_count":109,"open_issues_count":15,"forks_count":20,"subscribers_count":10,"default_branch":"master","last_synced_at":"2024-11-18T18:18:55.559Z","etag":null,"topics":["complexes","enzyme-ptm","networks","networks-biology","omnipath","pathways","proteins"],"latest_commit_sha":null,"homepage":"https://r.omnipathdb.org/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/saezlab.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","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":"2018-11-09T16:13:50.000Z","updated_at":"2024-11-17T14:29:30.000Z","dependencies_parsed_at":"2023-02-06T04:46:26.692Z","dependency_job_id":"49899fa5-7037-4988-898b-b6ab243aa637","html_url":"https://github.com/saezlab/OmnipathR","commit_stats":{"total_commits":1106,"total_committers":10,"mean_commits":110.6,"dds":0.09041591320072329,"last_synced_commit":"577f30d957385a873ef828a2cb99950941a9016b"},"previous_names":[],"tags_count":29,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FOmnipathR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FOmnipathR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FOmnipathR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FOmnipathR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/OmnipathR/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":226393033,"owners_count":17617995,"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":["complexes","enzyme-ptm","networks","networks-biology","omnipath","pathways","proteins"],"created_at":"2024-11-25T20:02:22.574Z","updated_at":"2024-11-25T20:02:27.453Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":["R"],"sub_categories":[],"readme":"\u003cimg src='man/figures/logo_omnipath.png' align='right' height='140'\u003e\n\n# OmnipathR\n\nAn `R` client for the **OmniPath** web service and many other resources.\n\n## Package contents\n\n* Client for the OmniPath web service\n* Functions for post-processing OmniPath data\n* Ensembl BioMart, UniProt and KEGG clients\n* Access to other databases (18+ resources, see below)\n* Integration to NicheNet, a method to infer ligand activities from\n   transcriptomics data\n\n### OmniPath web service client\n\n*OmnipathR* retrieves the data from the OmniPath web service at\n\n  \u003chttps://omnipathdb.org/\u003e\n\nThe web service implements a very simple REST-style API. This package makes\nrequests by the HTTP protocol to retrieve the data. Hence, fast Internet\naccess is required for a proper use of *OmnipathR*.\n\n#### What is OmniPath?\n\nOmniPath is a database of:\n\n* Protein-protein, TF target and miRNA-mRNA interactions\n* Enzyme-PTM relationships\n* Protein complexes\n* Annotations of protein function, structure, localization, expression\n* Intercellular communication roles of proteins\n\nTo learn more about OmniPath, you can visit its [website][1], or read our\nrecent [publication][4] or our first [paper from 2016][5], especially its\n[supplementary material][6].\n\n\n### Access to further resources\n\nThe package provides access to a number of other databases: BioPlex,\nConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS),\nHarmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway,\nPathway Commons, PrePPI, Ramilowski et al. 2015, RegNetwork, ReMap,\nTF census, TRRUST and Vinayagam et al. 2011.\n\n## Documentation\n\nThe latest version of the reference manual is available from\n\u003chttps://static.omnipathdb.org/omnipathr_manual.pdf\u003e. Tutorials can be\nfound at \u003chttps://workflows.omnipathdb.org/\u003e. Scroll down for quick start\nexamples.\n\n## OmniPath query types\n\nWe provide here a brief summary of the data available through *OmnipathR*.\n*OmnipathR* provides access to 5 types of queries:\n\n1. **Interactions**: protein-protein interactions from different datasets.\n2. **Enzyme-substrate**: enzyme-PTM (post-translational modification)\n    relationships.\n3. **Complexes**: comprehensive database of more than 22000 protein complexes.\n4. **Annotations**: large variety of data about protein and complex\n    features.\n5. **Intercell**: information on the roles in inter-cellular signaling.\n\nFor more detailed information, we recommend you to visit the following\nsites:\n\n  \u003chttps://omnipathdb.org/\u003e\n\n  \u003chttps://omnipathdb.org/info\u003e\n\n  \u003chttps://github.com/saezlab/pypath/blob/master/webservice.rst\u003e\n\n  \u003chttps://saezlab.github.io/OmnipathR/articles/omnipath_intro.html\u003e\n\n\n## Installation\n\nFirst of all, you need a current version of `R` (\u003chttps://r-project.org\u003e).\n\n### From Bioconductor\n*OmnipathR* is a freely available package deposited on *Bioconductor* and\n*Github*:\n(\u003chttps://bioconductor.org/\u003e, \u003chttps://github.com/saezlab/OmnipathR\u003e).\n\nYou can install it by running the following commands on a `R` console:\n\n```{r}\nif (!requireNamespace('BiocManager', quietly = TRUE))\n    install.packages('BiocManager')\n\n## Last release in Bioconductor\nBiocManager::install('OmnipathR', version = '3.12')\n## Development version with the latest updates\nBiocManager::install('OmnipathR', version = 'devel')\n```\n\n### From github\n\nWe add new features to OmnipathR way more often than the Bioconductor release\nfrequency. To make use of the recent developments, you can use `devtools` to\ninstall the package directly from github:\n\n```{r}\nrequire(devtools)\ninstall_github('saezlab/OmnipathR')\n```\n\n## Getting started and some usage examples\nTo get started, we strongly recommend to read our main vignette in order to deal\nwith the different types of queries and handle the data they return:\n\n  \u003chttps://saezlab.github.io/OmnipathR/articles/omnipath_intro.html\u003e\n\nYou can also check the manual:\n\n  \u003chttps://saezlab.github.io/OmnipathR/reference/index.html\u003e\n\nIn addition, we provide here some examples for a quick start:\n\n```{r}\nlibrary(OmnipathR)\n```\n\nDownload human protein-protein interactions from the specified resources:\n\n```{r}\ninteractions \u003c- omnipath(\n    resources = c('SignaLink3', 'PhosphoSite', 'SIGNOR')\n)\n```\n\n\nDownload human enzyme-PTM relationships from the specified resources:\n\n```{r}\nenzsub \u003c- enzyme_substrate(resources = c('PhosphoSite', 'SIGNOR'))\n```\n\nConvert both data frames into networks (`igraph` objects)\n```{r}\nptms_g = ptms_graph(ptms = enzsub)\nOPI_g = interaction_graph(interactions = interactions)\n```\n\nPrint some interactions in a nice format:\n```{r}\nprint_interactions(head(interactions))\n\n          source interaction         target n_resources n_references\n4    SRC (P12931)  ==( + )==\u003e TRPV1 (Q8NER1)           9            6\n2  PRKG1 (Q13976)  ==( - )==\u003e TRPC6 (Q9Y210)           7            5\n1  PRKG1 (Q13976)  ==( - )==\u003e TRPC3 (Q13507)           9            2\n5    LYN (P07948)  ==( + )==\u003e TRPV4 (Q9HBA0)           9            2\n6  PTPN1 (P18031)  ==( - )==\u003e TRPV6 (Q9H1D0)           3            2\n3 PRKACA (P17612)  ==( + )==\u003e TRPV1 (Q8NER1)           6            1\n```\n\nFind interactions between a specific kinase and a specific substrate:\n```{r}\nprint_interactions(dplyr::filter(enzsub,enzyme_genesymbol=='MAP2K1',\n  substrate_genesymbol=='MAPK3'))\n\n           enzyme interaction           substrate    modification n_resources\n1 MAP2K1 (Q02750)       ====\u003e MAPK3_Y204 (P27361) phosphorylation           8\n2 MAP2K1 (Q02750)       ====\u003e MAPK3_T202 (P27361) phosphorylation           8\n3 MAP2K1 (Q02750)       ====\u003e MAPK3_Y210 (P27361) phosphorylation           2\n4 MAP2K1 (Q02750)       ====\u003e MAPK3_T207 (P27361) phosphorylation           2\n\n```\n\nFind the shortest paths on the directed network between proteins:\n```{r}\nprint_path_es(shortest_paths(OPI_g,from = 'TYRO3',to = 'STAT3',\n    output = 'epath')$epath[[1]],OPI_g)\n\n           source interaction          target n_resources n_references\n1  TYRO3 (Q06418)  ==( ? )==\u003e   AKT1 (P31749)           2            0\n2   AKT1 (P31749)  ==( - )==\u003e DAB2IP (Q5VWQ8)           3            1\n3 DAB2IP (Q5VWQ8)  ==( - )==\u003e  STAT3 (P40763)           1            1\n```\n\nFind all shortest paths between proteins:\n```{r}\nprint_path_vs(all_shortest_paths(OPI_g,from = 'DYRK2',to = 'MAPKAPK2')$res,OPI_g)\nPathway 1: DYRK2 -\u003e TBK1 -\u003e NFKB1 -\u003e MAP3K8 -\u003e MAPK3 -\u003e MAPKAPK2\nPathway 2: DYRK2 -\u003e TBK1 -\u003e AKT3 -\u003e MAP3K8 -\u003e MAPK3 -\u003e MAPKAPK2\nPathway 3: DYRK2 -\u003e TBK1 -\u003e AKT2 -\u003e MAP3K8 -\u003e MAPK3 -\u003e MAPKAPK2\nPathway 4: DYRK2 -\u003e TBK1 -\u003e AKT1 -\u003e MAP3K8 -\u003e MAPK3 -\u003e MAPKAPK2\nPathway 5: DYRK2 -\u003e TBK1 -\u003e AKT3 -\u003e PEA15 -\u003e MAPK3 -\u003e MAPKAPK2\nPathway 6: DYRK2 -\u003e TBK1 -\u003e AKT2 -\u003e PEA15 -\u003e MAPK3 -\u003e MAPKAPK2\n.....\n```\n\n## Alternatives\n\n### Python\n\nA similar web service client is available for Python:\n\n    \u003chttps://github.com/saezlab/omnipath\u003e\n\n### Cytoscape\n\nThe OmniPath Cytoscape app provides access to the interactions, enzyme-PTM\nrelationships and some of the annotations:\n\n    \u003chttps://apps.cytoscape.org/apps/omnipath\u003e\n\n### Customization\n\nThe [*pypath*](https://github.com/saezlab/pypath) Python module is a tool for\nbuilding the OmniPath databases in a fully customizable way. We recommend to\nuse pypath if you want to:\n\n* Tailor the database building to your needs\n* Include resources not available in the public web service\n* Use the rich Python APIs available for the database objects\n* Make sure the data from the original sources is the most up-to-date\n* Use the methods in ``pypath.inputs`` to download data from resources\n* Use the various extra tools in ``pypath.utils``, e.g. for identifier\n  translation, homology translation, querying Gene Ontology, working with\n  protein sequences, processing BioPAX, etc.\n\nWith *pypath* it's also possible to run your own web service and serve your\ncustom databases to the *OmnipathR* R client and the *omnipath* Python client.\n\n## Feedbacks, bug reports, features\n\nFeedbacks and bug reports are always very welcome!\n\nPlease use the Github issue page to report bugs or for questions:\n\n  \u003chttps://github.com/saezlab/OmnipathR/issues\u003e\n\nMany thanks for using *OmnipathR*!\n\n\n[1]: https://omnipathdb.org/\n[2]: https://apps.cytoscape.org/apps/omnipath\n[3]: https://github.com/saezlab/pypath\n[4]: https://www.embopress.org/doi/full/10.15252/msb.20209923\n[5]: https://www.nature.com/articles/nmeth.4077\n[6]: https://static-content.springer.com/esm/art%3A10.1038%2Fnmeth.4077/MediaObjects/41592_2016_BFnmeth4077_MOESM495_ESM.pdf\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2FOmnipathR","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2FOmnipathR","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2FOmnipathR/lists"}