{"id":22731090,"url":"https://github.com/genentech/epiregulon","last_synced_at":"2025-07-11T09:38:34.441Z","repository":{"id":208522385,"uuid":"562712848","full_name":"Genentech/epiregulon","owner":"Genentech","description":"Construct gene regulatory networks and infer transcription factor (TF) activity in single cells by integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data.","archived":false,"fork":false,"pushed_at":"2023-11-29T04:14:44.000Z","size":221410,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-05T03:27:56.272Z","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":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Genentech.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":"2022-11-07T05:01:11.000Z","updated_at":"2024-12-08T03:49:03.000Z","dependencies_parsed_at":"2023-11-21T23:28:20.726Z","dependency_job_id":"877d85d1-d67c-468e-bee6-14c6226a8a62","html_url":"https://github.com/Genentech/epiregulon","commit_stats":null,"previous_names":["genentech/epiregulon"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fepiregulon","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fepiregulon/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fepiregulon/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fepiregulon/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Genentech","download_url":"https://codeload.github.com/Genentech/epiregulon/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246264484,"owners_count":20749473,"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":"2024-12-10T19:19:24.117Z","updated_at":"2025-03-30T01:29:50.219Z","avatar_url":"https://github.com/Genentech.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"![plot](inst/epiregulon_logo.png)\u003cbr\u003e\n\n# Introduction\n\nGene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and cell states. The main function of the epiregulon package is to construct gene regulatory networks and infer transcription factor (TF) activity in single cells by integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data.\n\nFor full documentation, please refer to the epiregulon [book](https://xiaosaiyao.github.io/epiregulon.book/).\n\nPreprint\nEpiregulon: Inference of single-cell transcription factor activity to dissect mechanisms of lineage plasticity and drug response\nTomasz Wlodarczyk, Aaron Lun, Diana Wu, Shreya Menon, Shushan Toneyan, Kerstin Seidel, Liang Wang, Jenille Tan, Shang-Yang Chen, Timothy Keyes, Aleksander Chlebowski, Yu Guo, Ciara Metcalfe, Marc Hafner, Christian W. Siebel, M. Ryan Corces, Robert Yauch, Shiqi Xie, Xiaosai Yao\nbioRxiv 2023.11.27.568955; doi: [https://doi.org/10.1101/2023.11.27.568955](https://www.biorxiv.org/content/10.1101/2023.11.27.568955v1)\n\n![plot](inst/epiregulon_schematics.svg) \nThere are three related packages. The core epiregulon package supports `SingleCellExperiment` objects. If the users would like to start from `ArchR` projects, they may choose to use `epiregulon.archr` package, which allows for the seamless integration with the [ArchR](https://www.archrproject.com/) package. Moreover, we provide a suite of tools in `epiregulon.extra` package for the enrichment analysis, visualization, and network analysis which can be run on the `epireglon` or `epiregulon.archr` output.\n\n# Installation\n\n```\n# install devtools\nif(!require(devtools)) install.packages(\"devtools\")\n\n# install basic epiregulon package\ndevtools::install_github(repo='xiaosaiyao/epiregulon')\n\n# install extended version of epiregulon\ndevtools::install_github(repo='xiaosaiyao/epiregulon.archr')\n\n# install extended version of epiregulon\ndevtools::install_github(repo='xiaosaiyao/epiregulon.extra')\n```\n\nExample data included in the tutorial are available from [scMultiome](https://bioconductor.org/packages/release/data/experiment/html/scMultiome.html) \n\n```\nif (!require(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"scMultiome\")\n```\n\n# Functions\nFunctions in the suite of Epiregulon packages\n![plot](inst/epiregulon_functions.png)\n\n\nContact: [Xiaosai Yao](mailto:yao.xiaosai@gene.com), Genentech Inc.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fepiregulon","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenentech%2Fepiregulon","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fepiregulon/lists"}