dose-response

The script uses the formula for the 4PL-Dose-Response-Curve for fitting:

    Y = Bottom + (Top - Bottom) / (1 + 10 ** (HillSlope * (lg EC50 - lg X)))

CAVE: Default unit is µM and confidence level is 0.05 (to change: use the python class manually)

Input:

• A csv file with doses and its corresponding responses

Output:

• A logarithmic dose-response plot of the fitted curce with standard error bars
• A csv file with the fitted parameters, their SD and the lower and upper bounds of the CI

Usage

1. Install DRC

pip install dose-response

2. Provide your data results in a CSV file without headers (Mark values to exclude with an * as suffix).

3. Execute DRC

    file: CSV file with data
    -d, --dose-col: Column index of doses: [Default: 0]
    -r, --response-cols: start and end index of response columns: [Default: every other column]
    -o, --out Output directory [Default: current working directory]
   
   
    drc DataFile -d DoseColumnIndex -r ResponseStartIndex ResponseEndIndex -o OutputDir
   
    drc demo/demo.csv -d 0 -r 1 4 -o demo
   

4. Plot is stored in OutputDirectory/DataFileBase_plot.png

    demo/demo_plot.png
   

4. Parameters are stored in OutputDirectory/DataFileBase_params.csv

    demo/demo_params.csv
   

Test

1. Create test data

    drc-test TestDataFile
   

2. Execute DRC

    drc TestDataFile
   

Acknowledgments

Thanks to yannabraham (https://gist.github.com/yannabraham/5f210fed773785d8b638)