{"id":24529005,"url":"https://github.com/saezlab/collectri","last_synced_at":"2025-04-14T17:10:52.259Z","repository":{"id":161011529,"uuid":"403639326","full_name":"saezlab/CollecTRI","owner":"saezlab","description":"Gene regulatory network containing signed transcription factor-target gene interactions","archived":false,"fork":false,"pushed_at":"2024-04-24T15:19:52.000Z","size":8438,"stargazers_count":73,"open_issues_count":0,"forks_count":7,"subscribers_count":7,"default_branch":"main","last_synced_at":"2025-03-28T05:51:01.844Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","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":"2021-09-06T13:48:15.000Z","updated_at":"2025-03-16T12:49:59.000Z","dependencies_parsed_at":"2023-10-04T15:21:19.734Z","dependency_job_id":"eeff15a2-1b9e-4e50-a5ee-cc2a3e54d4f4","html_url":"https://github.com/saezlab/CollecTRI","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%2FCollecTRI","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCollecTRI/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCollecTRI/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCollecTRI/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/CollecTRI/tar.gz/refs/heads/main","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":"2025-01-22T07:34:25.699Z","updated_at":"2025-04-14T17:10:52.218Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CollecTRI: **Collec**tion of **T**ranscriptional **R**egulatory **I**nteractions \u003cimg src=\"man/figures/CollecTRI_logo.png\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n\u003c!-- badges: end --\u003e\n\n## Overview\nThe CollecTRI-derived regulons contain signed transcription factor (TF) - target gene \ninteractions compiled from 12 different resources. This collection provides \nan increased coverage of transcription factors and was benchmarked against \nother known GRNs, showing a superior performance in identifying perturbed TFs \nbased on gene expression data using the knockTF data sets.\n\n\u003cp align=\"center\" width=\"100%\"\u003e\n\u003cimg src=\"man/figures/overview.png\" align=\"center\" width=\"550\"\u003e\n\u003c/p\u003e\n\n## Data availability \nThe CollecTRI regulons are available in the [DoRothEA](https://saezlab.github.io/dorothea/) and [decoupler](https://saezlab.github.io/decoupleR/) packages through [OmniPath](https://omnipathdb.org/).\nA tutorial on how to perform TF activity estimation using CollecTRI is available in [R](https://saezlab.github.io/decoupleR/articles/tf_bk.html) and [python](https://decoupler-py.readthedocs.io/en/latest/notebooks/dorothea.html). \n\nTo load the CollecTRI regulons through R or python you can use the following lines:\n```r\n# processed regulons\ndecoupleR::get_collectri(organism='human', split_complexes=FALSE)\n\n# raw regulons\nOmnipathR::collectri(organism=9606L, genesymbols=TRUE, loops=TRUE)\n```\n\n```python\n# processed regulons\nimport decoupler as dc\ndc.get_collectri(organism='human', split_complexes=False)\n\n# raw regulons\nimport omnipath as op\nop.interactions.CollecTRI.get(genesymbols=True, organism=9606L, loops=True)\n```\n\n## Resources included in CollecTRI\nExTRI, HTRI, TRRUST, TFActS, IntAct, SIGNOR, CytReg, GEREDB, Pavlidis, DoRothEA A, NTNU curations\n\n## Scripts\nFor more information about the CollecTRI-derived regulons, please check out the following scripts:\n\n- [Construction of CollecTRI regulons](https://github.com/saezlab/CollecTRI/tree/main/scripts/CollecTRI)\n- [Benchmark](https://github.com/saezlab/CollecTRI/tree/main/scripts/benchmark)\n  - [Systematic comparison](https://github.com/saezlab/CollecTRI/blob/main/scripts/benchmark/02_benchmark.ipynb)\n  - [Evaluation of binding weights](https://github.com/saezlab/CollecTRI/blob/main/scripts/benchmark/03_benchmark_weights.ipynb)\n  - [Statistical evaluation](https://github.com/saezlab/CollecTRI/blob/main/scripts/benchmark/05_statistics.R)\n- [Case study](https://github.com/saezlab/CollecTRI/blob/main/scripts/casestudy/case_study.R)\n- [Manuscript figures](https://github.com/saezlab/CollecTRI/blob/main/scripts/figures/figures_manuscript.R)\n\nIf you are interested in the construction of the CollecTRI meta-resource check\nout this [repository](https://github.com/Rbbt-Workflows/ExTRI)\n\n## License\nThe CollecTRI-derived regulons are freely available.\nThe original licenses of all resources included in CollecTRI can be found [here](https://github.com/saezlab/pypath/blob/master/pypath/resources/data/resources.json)\n\n\n## Citation\n\u003e Müller-Dott, S., Tsirvouli, E., Vazquez, M., Ramirez Flores, R. O., Badia-I-Mompel, P., Fallegger, R., Türei, D., Lægreid, A., \u0026 Saez-Rodriguez, J. (2023).\n\u003e Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities.\n\u003e Nucleic Acids Research. https://doi.org/10.1093/nar/gkad841\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fcollectri","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fcollectri","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fcollectri/lists"}