{"id":24529038,"url":"https://github.com/saezlab/dorothea","last_synced_at":"2025-03-02T14:19:12.513Z","repository":{"id":20514629,"uuid":"86356783","full_name":"saezlab/dorothea","owner":"saezlab","description":"R package to access DoRothEA's regulons","archived":false,"fork":false,"pushed_at":"2024-02-24T12:21:16.000Z","size":412441,"stargazers_count":142,"open_issues_count":5,"forks_count":27,"subscribers_count":15,"default_branch":"master","last_synced_at":"2025-02-22T20:34:04.020Z","etag":null,"topics":["bioconductor-package","functional-analysis","gene-expression","regulons","tf-activities","transcription-factor"],"latest_commit_sha":null,"homepage":"https://saezlab.github.io/dorothea/","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":"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":"2017-03-27T16:10:28.000Z","updated_at":"2025-01-28T09:30:06.000Z","dependencies_parsed_at":"2022-08-07T09:16:08.301Z","dependency_job_id":"8370ae3e-f805-4d63-aff4-9ead7facbb03","html_url":"https://github.com/saezlab/dorothea","commit_stats":{"total_commits":239,"total_committers":8,"mean_commits":29.875,"dds":"0.10878661087866104","last_synced_commit":"840f4d9d1650b434a9035a3b9874c16b8d3a59f1"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fdorothea","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fdorothea/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fdorothea/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fdorothea/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/dorothea/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241516035,"owners_count":19975146,"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":["bioconductor-package","functional-analysis","gene-expression","regulons","tf-activities","transcription-factor"],"created_at":"2025-01-22T07:34:31.290Z","updated_at":"2025-03-02T14:19:12.477Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DoRothEA: collection of human and mouse regulons \u003cimg src=\"man/figures/tool_logo.png\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/saezlab/dorothea/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/saezlab/dorothea/actions)\n[![BioC status](http://bioconductor.org/shields/build/release/data-experiment/dorothea.svg)](https://bioconductor.org/checkResults/release/data-experiment-LATEST/dorothea)\n[![codecov](https://codecov.io/gh/saezlab/dorothea/branch/master/graph/badge.svg)](https://codecov.io/gh/saezlab/dorothea)\n![GitHub](https://img.shields.io/github/license/saezlab/dorothea)\n\u003c!-- badges: end --\u003e\n\n## Overview\nDoRothEA is a gene regulatory network (GRN) containing signed transcription factor\n(TF) - target gene interactions. DoRothEA regulons, the collection of a TF and\nits transcriptional targets, were curated and collected from different types of\nevidence for both human and mouse. A confidence level was assigned to each \nTF-target interaction based on the number of supporting evidence. \n\n\u003cimg src=\"man/figures/overview.png\" align=\"center\" width=\"600\"\u003e\n\nThese regulons, coupled with any statistical method, can be\nused to infer TF activities from bulk or single-cell transcriptomics. \n\nThis is an R package for storing the regulons. To infer TF\nactivities, please check out\n[decoupleR](https://doi.org/10.1093/bioadv/vbac016), available in\n[R](https://saezlab.github.io/decoupleR/) or\n[python](https://github.com/saezlab/decoupler-py).\n\n## Installation\n\nDoRothEA is available in\n[Bioconductor](http://bioconductor.org/packages/release/data/experiment/html/dorothea.html). \nIn addition, one can install the development version from the Github repository:\n```r\n## To install the package from Bioconductor\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"dorothea\")\n\n## To install the development version from the Github repo:\ndevtools::install_github(\"saezlab/dorothea\")\n```\n\n## Updates\n\nSince the original release, we have implemented some extensions in DoRothEA:\n\n1. **Extension to mouse**:\n  Originally DoRothEA was developed for the application to human data. \n  In a benchmark study we showed that DoRothEA is also applicable to mouse data, \n  as described in \n  [Holland et al., 2019](https://doi.org/10.1016/j.bbagrm.2019.194431). \n  Accordingly, we included new parameters to run mouse version of DoRothEA by \n  transforming the human genes to their mouse orthologs.\n2. **Extension to single-cell RNA-seq data**:\n  We showed that DoRothEA can be applied to scRNA-seq data, as described in\n  [Holland et al., 2020](https://doi.org/10.1186/s13059-020-1949-z)\n\n3. **Extension to other databases**\n  We have released a new literature based GRN with increased coverage and better\n  performance at identifying perturbed TFs, called [CollecTRI](https://github.com/saezlab/CollecTRI).\n  We encourage users to use CollecTRI instead of DoRothEA. Vignettes on how to\n  obtain activities are available at the [decoupleR package](https://saezlab.github.io/decoupleR/).\n\n## License\nDoRothEA is intended only for academic use as in contains resources\nwhose licenses don't permit commercial use. However, we developed a non-academic\nversion of DoRothEA by removing those resources (mainly TRED from the curated\ndatabases). You can find the non-academic package with the regulons [here](https://github.com/saezlab/dorothea/tree/non-academic).\n\n## Citation\nIf you use the DoRothEA resource, please cite:\n\n\u003e Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J.\nBenchmark and integration of resources for the estimation of human\ntranscription factor activities. _Genome Research._ 2019. DOI: [10.1101/gr.240663.118](https://doi.org/10.1101/gr.240663.118).\n\nIf you infer TF activities, please cite:\n\n\u003e Badia-i-Mompel P., Vélez Santiago J., Braunger J., Geiss C., Dimitrov\n  D., Müller-Dott S., Taus P., Dugourd A., Holland C.H., Ramirez Flores R.O.\n  and Saez-Rodriguez J. decoupleR: Ensemble of computational methods to\n  infer biological activities from omics data. 2022. _Bioinformatics Advances_.\n  DOI: [10.1093/bioadv/vbac016](https://doi.org/10.1093/bioadv/vbac016)\n\nIf you use the CollecTRI resource, please cite:\n\n\u003e Müller-Dott S., Tsirvouli E., Vázquez M., Ramirez Flores R.O.,\n  Badia-i-Mompel P., Fallegger R., Lægreid A. and Saez-Rodriguez J.\n  Expanding the coverage of regulons from high-confidence prior knowledge for\n  accurate estimation of transcription factor activities. _bioRxiv_. 2023. DOI:\n  [10.1101/2023.03.30.534849](https://doi.org/10.1101/2023.03.30.534849)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fdorothea","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fdorothea","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fdorothea/lists"}