Overview

# Examples

Example notebooks demostrating the use of copairs.

Installation

To install dependencies for running examples, run:

pip install copairs[demo]

Running examples

cd docs/examples
jupyter notebook

List of examples

We show how to use copairs for:

• grouping profiles based on their metadata
• calculating mAP to assess phenotypic activity of perturbations
• calculating mAP to assess phenotypic consistency of perturbations
• estimating null size for mAP p-value calculation

Data used

In these examples, we used a single plate of profiles from the dataset "cpg0004" (aka LINCS), which contains Cell Painting images of 1,327 small-molecule perturbations of A549 human cells. The wells on each plate were perturbed with 56 different compounds in six different doses.

Way, G. P. et al. Morphology and gene expression profiling provide complementary information for mapping cell state. Cell Syst 13, 911–923.e9 (2022).