{"id":24360486,"url":"https://github.com/simonsfoundation/th17_trn_networks","last_synced_at":"2025-10-06T14:23:17.143Z","repository":{"id":98237925,"uuid":"121539059","full_name":"simonsfoundation/Th17_TRN_Networks","owner":"simonsfoundation","description":"Data and notebooks for \"Leveraging ATAC-seq data for transcriptional regulatory inference in Th17 Cells\" by Miraldi et al.","archived":false,"fork":false,"pushed_at":"2019-02-20T19:10:57.000Z","size":108497,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-01-18T21:32:38.786Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/simonsfoundation.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":"2018-02-14T17:22:30.000Z","updated_at":"2024-12-06T02:04:51.000Z","dependencies_parsed_at":"2023-05-18T21:45:41.014Z","dependency_job_id":null,"html_url":"https://github.com/simonsfoundation/Th17_TRN_Networks","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2FTh17_TRN_Networks","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2FTh17_TRN_Networks/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2FTh17_TRN_Networks/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2FTh17_TRN_Networks/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/simonsfoundation","download_url":"https://codeload.github.com/simonsfoundation/Th17_TRN_Networks/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243188204,"owners_count":20250452,"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":"2025-01-18T21:30:01.669Z","updated_at":"2025-10-06T14:23:17.070Z","avatar_url":"https://github.com/simonsfoundation.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/simonsfoundation/Th17_TRN_Networks/master)\n\n# Th17_TRN_Networks\n\nThis repository contains interactive visualization of transcriptional regulatory networks and gene expression data from:\n\n[Miraldi et al., Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells](https://genome.cshlp.org/content/early/2019/02/19/gr.238253.118).\n\n\n\nThe repository has been designed to run in the cloud based Binder service.\nClick the binder link above to launch a binder container running the notebooks\n\n\nThe repository is designed to use \n[`repo2docker`](https://repo2docker.readthedocs.io/en/latest/)\nto build a `docker` container which includes\nthe code for running the analysis and all needed dependencies.\nThe `repo2docker` tool requires the `docker` infrastructure\nand Python 3 to run.  See the \n[installation instructions](https://repo2docker.readthedocs.io/en/latest/install.html).\n\nTo build the docker image from the command line\n\n```bash\njupyter-repo2docker --no-run \\\n    --image-name th17 \\\n    https://github.com/simonsfoundation/Th17_TRN_Networks\n```\n\nTo run the image after it has been built use `docker run`:\n\n```bash\ndocker run -it --rm -p 8888:8888 th17:latest\n```\n\nWhen the docker instance starts up the log output looks like this:\n\n```\n[I 19:34:40.443 NotebookApp] Writing notebook server cookie secret to /home/rstudio/.local/share/jupyter/runtime/notebook_cookie_secret\n[I 19:34:40.935 NotebookApp] Serving notebooks from local directory: /home/rstudio\n[I 19:34:40.935 NotebookApp] 0 active kernels\n[I 19:34:40.935 NotebookApp] The Jupyter Notebook is running at:\n[I 19:34:40.935 NotebookApp] http://0.0.0.0:8888/?token=7baca1829f0665df26adf9943c6f04279647171eb3ffd12c\n[I 19:34:40.935 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).\n[W 19:34:40.935 NotebookApp] No web browser found: could not locate runnable browser.\n[C 19:34:40.936 NotebookApp] \n    \n    Copy/paste this URL into your browser when you connect for the first time,\n    to login with a token:\n        http://0.0.0.0:8888/?token=7baca1829f0665df26adf9943c6f04279647171eb3ffd12c\n```\n\nPaste the `http:...` URL into your browser including your token (which will be different\nfrom the one shown above) to connect to the Jupyter server.  \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsimonsfoundation%2Fth17_trn_networks","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsimonsfoundation%2Fth17_trn_networks","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsimonsfoundation%2Fth17_trn_networks/lists"}