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https://github.com/trfore/chat-project
Analysis files from Fore et al. 2020
https://github.com/trfore/chat-project
cerebellar-granule-cell neuroscience
Last synced: about 2 months ago
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Analysis files from Fore et al. 2020
- Host: GitHub
- URL: https://github.com/trfore/chat-project
- Owner: trfore
- License: mit
- Created: 2018-07-25T16:52:26.000Z (over 6 years ago)
- Default Branch: main
- Last Pushed: 2023-07-27T17:45:04.000Z (over 1 year ago)
- Last Synced: 2024-10-21T15:32:32.640Z (3 months ago)
- Topics: cerebellar-granule-cell, neuroscience
- Language: R
- Homepage: https://doi.org/10.1523/JNEUROSCI.2148-19.2020
- Size: 10.7 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# ChAT Project
## Introduction
These are the analysis files used in the following publication:
- 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
## How to Use
### Requirements
- R language: [R] (R >= 3.2.0)
- R package: [matools]
- R package: [googlesheets4] (required if running the scripts as CRON jobs)
- R package: [utils] (core package - required if running the scripts as CRON jobs)
- RStudio: [RStudio] (IDE for interactive analysis)
### Running Workflows
1. The workflow scripts in the repository are fully automated and expect the directory structure as follows:
```sh
├── analysis_scripts
│ ├── evoked_ap_analysis.R
│ └── evoked_psp_analysis.R
├── data
│ ├── cell_attached_grc_evoked_ap
│ │ ├── chat_evoked_ap_parameters.csv
│ │ └── data
│ │ ├── rec000000.ASC
│ │ ├── rec000000.txt
│ │ ...
│ │ ├── rec00000x.ASC
│ │ └── rec00000x.txt
│ └── evoked_psp
│ ├── chat_evoked_psp_parameters.csv
│ └── data
│ ├── rec000000.ASC
│ ...
│ └── rec00000x.ASC
```
2. Clone the repository and change into the `analysis_scripts` directory
```sh
$ git clone https://github.com/trfore/chat-project.git
$ cd chat-project
```
3. Run the scripts. PDF figures are placed within the parent directory, `chat-project`.
```R
# Evoked Granule Cell Action Potential Analysis
Rscript analysis_scripts/evoked_ap_analysis.R
# Evoked Post-Synaptic Potential Analysis
Rscript analysis_scripts/evoked_psp_analysis.R
```
4. Alternatively, interactively run these scripts within [RStudio].
### Running Workflows as CRON jobs
1. Modify a workflow by changing the following:
```R
# Project Data Processing ----
# Local data files
data_path <- paste(getwd(), "data/evoked_psp", sep = "/")
data_folder <- paste(data_path, "data", sep = "/")
# Option 1: Using local parameter sheet
data_parameters <- paste(data_path, "chat_evoked_psp_parameters.csv", sep = "/")
# Option 2: Using publicly shared Google Sheet
googlesheets4::gs4_deauth()
public_sheet <- "https://docs.google.com/spreadsheets/d/YOUR_SHEET_HASH_HERE/edit?usp=sharing"
data_parameters <-
googlesheets4::read_sheet(public_sheet)
# Import the parameters
import_experiment_parameters(data_parameters)
```
2. Create a cron job
```sh
# crontab file
# run daily at midnight
0 0 * * * cd /home/chat-project/analysis_scripts; Rscript evoked_ap_analysis.R >/dev/null 2>&1
# run daily at 12:30 am
30 0 * * * cd /home/chat-project/analysis_scripts; Rscript evoked_psp_analysis.R >/dev/null 2>&1
```
# Authors
- Taylor Fore (https://github.com/trfore)
# References
- Fore et al. 2020
- https://github.com/trfore/matools
- https://github.com/trfore/chat-project
- https://github.com/trfore/chatmodel
- https://www.r-project.org/
- https://www.rstudio.com/
## R packages
- https://github.com/tidyverse/googlesheets4/
- https://github.com/HenrikBengtsson/R.utils
[googlesheets4]: https://github.com/tidyverse/googlesheets4/
[matools]: https://github.com/trfore/matools
[R]: https://www.r-project.org/
[RStudio]: https://www.rstudio.com/
[utils]: https://github.com/HenrikBengtsson/R.utils