{"id":15602221,"url":"https://github.com/trfore/chat-project","last_synced_at":"2025-10-26T10:31:54.387Z","repository":{"id":184284822,"uuid":"142328783","full_name":"trfore/chat-project","owner":"trfore","description":"Analysis files from Fore et al. 2020","archived":false,"fork":false,"pushed_at":"2023-07-27T17:45:04.000Z","size":11,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-02-04T13:44:09.874Z","etag":null,"topics":["cerebellar-granule-cell","neuroscience"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1523/JNEUROSCI.2148-19.2020","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/trfore.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}},"created_at":"2018-07-25T16:52:26.000Z","updated_at":"2023-07-27T17:51:34.000Z","dependencies_parsed_at":"2023-07-27T20:10:22.357Z","dependency_job_id":null,"html_url":"https://github.com/trfore/chat-project","commit_stats":null,"previous_names":["trfore/chat-project"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trfore%2Fchat-project","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trfore%2Fchat-project/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trfore%2Fchat-project/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trfore%2Fchat-project/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/trfore","download_url":"https://codeload.github.com/trfore/chat-project/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246187219,"owners_count":20737460,"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":["cerebellar-granule-cell","neuroscience"],"created_at":"2024-10-03T02:40:42.011Z","updated_at":"2025-10-26T10:31:54.299Z","avatar_url":"https://github.com/trfore.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ChAT Project\n\n## Introduction\n\nThese are the analysis files used in the following publication:\n\n- Taylor R Fore et al. \"Acetylcholine modulates cerebellar granule cell spiking by regulating the balance of synaptic excitation and inhibition\" Journal of Neuroscience 1 April 2020, DOI: https://doi.org/10.1523/JNEUROSCI.2148-19.2020\n\n## How to Use\n\n### Requirements\n\n- R language: [R] (R \u003e= 3.2.0)\n- R package: [matools]\n- R package: [googlesheets4] (required if running the scripts as CRON jobs)\n- R package: [utils] (core package - required if running the scripts as CRON jobs)\n- RStudio: [RStudio] (IDE for interactive analysis)\n\n### Running Workflows\n\n1. The workflow scripts in the repository are fully automated and expect the directory structure as follows:\n\n```sh\n├── analysis_scripts\n│   ├── evoked_ap_analysis.R\n│   └── evoked_psp_analysis.R\n├── data\n│   ├── cell_attached_grc_evoked_ap\n│   │   ├── chat_evoked_ap_parameters.csv\n│   │   └── data\n│   │       ├── rec000000.ASC\n│   │       ├── rec000000.txt\n│   │       ...\n│   │       ├── rec00000x.ASC\n│   │       └── rec00000x.txt\n│   └── evoked_psp\n│       ├── chat_evoked_psp_parameters.csv\n│       └── data\n│           ├── rec000000.ASC\n│           ...\n│           └── rec00000x.ASC\n```\n\n2. Clone the repository and change into the `analysis_scripts` directory\n\n```sh\n$ git clone https://github.com/trfore/chat-project.git\n$ cd chat-project\n```\n\n3. Run the scripts. PDF figures are placed within the parent directory, `chat-project`.\n\n```R\n# Evoked Granule Cell Action Potential Analysis\nRscript analysis_scripts/evoked_ap_analysis.R\n\n# Evoked Post-Synaptic Potential Analysis\nRscript analysis_scripts/evoked_psp_analysis.R\n```\n\n4. Alternatively, interactively run these scripts within [RStudio].\n\n### Running Workflows as CRON jobs\n\n1. Modify a workflow by changing the following:\n\n```R\n# Project Data Processing ----\n# Local data files\ndata_path \u003c- paste(getwd(), \"data/evoked_psp\", sep = \"/\")\ndata_folder \u003c- paste(data_path, \"data\", sep = \"/\")\n\n# Option 1: Using local parameter sheet\ndata_parameters \u003c- paste(data_path, \"chat_evoked_psp_parameters.csv\", sep = \"/\")\n\n# Option 2: Using publicly shared Google Sheet\ngooglesheets4::gs4_deauth()\npublic_sheet \u003c- \"https://docs.google.com/spreadsheets/d/YOUR_SHEET_HASH_HERE/edit?usp=sharing\"\ndata_parameters \u003c-\n  googlesheets4::read_sheet(public_sheet)\n\n# Import the parameters\nimport_experiment_parameters(data_parameters)\n```\n\n2. Create a cron job\n\n```sh\n# crontab file\n# run daily at midnight\n0 0 * * * cd /home/chat-project/analysis_scripts; Rscript evoked_ap_analysis.R \u003e/dev/null 2\u003e\u00261\n# run daily at 12:30 am\n30 0 * * * cd /home/chat-project/analysis_scripts; Rscript evoked_psp_analysis.R \u003e/dev/null 2\u003e\u00261\n```\n\n# Authors\n\n- Taylor Fore (https://github.com/trfore)\n\n# References\n\n- Fore et al. 2020\n- https://github.com/trfore/matools\n- https://github.com/trfore/chat-project\n- https://github.com/trfore/chatmodel\n- https://www.r-project.org/\n- https://www.rstudio.com/\n\n## R packages\n\n- https://github.com/tidyverse/googlesheets4/\n- https://github.com/HenrikBengtsson/R.utils\n\n[googlesheets4]: https://github.com/tidyverse/googlesheets4/\n[matools]: https://github.com/trfore/matools\n[R]: https://www.r-project.org/\n[RStudio]: https://www.rstudio.com/\n[utils]: https://github.com/HenrikBengtsson/R.utils\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftrfore%2Fchat-project","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftrfore%2Fchat-project","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftrfore%2Fchat-project/lists"}