{"id":20081085,"url":"https://github.com/trangdata/neuro-penn","last_synced_at":"2026-03-05T07:02:34.390Z","repository":{"id":95112884,"uuid":"309727963","full_name":"trangdata/neuro-penn","owner":"trangdata","description":null,"archived":false,"fork":false,"pushed_at":"2021-01-28T15:16:24.000Z","size":27147,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-02T13:27:54.122Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/trangdata.png","metadata":{"files":{"readme":"readme.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2020-11-03T15:24:57.000Z","updated_at":"2021-01-28T15:16:27.000Z","dependencies_parsed_at":"2023-05-26T18:15:23.707Z","dependency_job_id":null,"html_url":"https://github.com/trangdata/neuro-penn","commit_stats":{"total_commits":87,"total_committers":2,"mean_commits":43.5,"dds":"0.25287356321839083","last_synced_commit":"3a41c31df581f4e316da4f6ccb99ffeec55fe6f3"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/trangdata/neuro-penn","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Fneuro-penn","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Fneuro-penn/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Fneuro-penn/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Fneuro-penn/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/trangdata","download_url":"https://codeload.github.com/trangdata/neuro-penn/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Fneuro-penn/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30113112,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-05T03:40:26.266Z","status":"ssl_error","status_checked_at":"2026-03-05T03:39:15.902Z","response_time":93,"last_error":"SSL_connect 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run?\n\n**Short answer: `elix-short-term.Rmd` and `elix-cpns.Rmd`** \n\nThe best way to run this analysis is to clone this repository on your local machine\n(please ensure you're in a directory where you want the repository to be downloaded):\n\n```git clone https://github.com/trang1618/neuro-penn.git```\n\nThen, go inside the repository:\n\n```cd neuro-penn```\n\nand make a copy of `elix-short-term.Rmd`, name it with your site name, for example:\n\n```cp elix-short-term.Rmd elix-short-term-penn.Rmd```\n\nThen, open the R project\n\n```open neuro-penn.Rproj```\n\nand navigate to the newly created file (e.g. `elix-short-term-penn.Rmd`) to modify the code to run on the data at your specific site.\n**Please be sure to change the second code chunk to read in your site-specific data, including replacing \"penn\" with your site name,** for example, `mysite = 'nwu'`.\nOnce everything runs, please hit the \"Knit\" button on top of the `.Rmd` file to create an `.html` file that will automatically be put into [`htmls/`](htmls/).\n\nKnit the `elix-cpns-[your_site_id].Rmd` similarly.\n\nFinally, please upload your results (in [`results/`](results/) and [`htmls/`](htmls/)) via a [pull request](https://github.com/trang1618/neuro-penn/pulls) or request @trang1618 to add you as a contributor.\n\nIf you run into any problem adapting this code to your data, let us (@meghutch and @trang1618) know via Slack or [submit an issue](https://github.com/trang1618/neuro-penn/issues/new).\n\n## Troubleshooting\n### Where is the `run_fish()` function?\n\nIt's under [`R/run_fish.R`](R/run_fish.R).\n\nWe also have other utility functions in the [`R/`](R/) directory.\nIf you did not clone the repo, you can simply download these files in the [`R/`](R/) directory and source them in the main 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