ephys-analysis-tools

Code base generating formatted data tables that streamlines data analysis process for ephys production metadata.

• Required: Anaconda Command Prompt

Authors:

• @ramr24

Installation:

1. Clone the repository in a directory of your choice.
2. Navigate to the directory of the cloned repository.

cd ephys-analysis-tools\

3. Create a new virtual environment (ephys-analysis-tools-env) from the .yml file.

conda env create -f environment.yml

4. Look below at Usage for detailed steps to run python scripts.

Usage: Batch Files

• Required: Location of Anaconda bat file --> C:\Users%USERNAME%\Anaconda3\Scripts\activate.bat

1. In File Explorer, navigate to the directory of the cloned repository.

cd ephys-analysis-tools\

2. Click on the desired .bat file to run the intended program.

Usage: Run Transcriptomics Reports through Anconda Command Prompt

*Run in Anaconda Command Prompt

1. Navigate to the directory of the cloned repository.

cd ephys-analysis-tools\src\run_scripts

2. Activate the specified virtual environment.

activate ephys-analysis-tools-env

3. Run the python scripts for daily/weekly transcriptomics reports.

python ivscc_daily_transcriptomics_report.py

python ivscc_weekly_transcriptomics_report.py

python hct_daily_transcriptomics_report.py

python hct_weekly_transcriptomics_report.py

4. Deactivate the specified virtual environment.

conda deactivate

Project Organization

├── README.md                                            <- The top-level README
├── .gitignore                                           <- Ignore file types
├── environment.yml                                      <- Requirements file
├── batch_files                                          <- Batch files
    ├── hct_transcriptomic_reports                       <- Batch files related to HCT transcriptomic reports
    ├── ivscc_data_generation                            <- Batch files related to IVSCC data generation
    └── ivscc_transcriptomic_reports                     <- Batch files related to IVSCC transcriptomic reports
├── src                                                  <- Source code
    ├── constants                                        <- JSON
    └── run_scripts                                      <- Python run scripts
        └── functions                                    <- Python function scripts