Processed Cell Painting Data for the LINCS Drug Repurposing Project

The repository stores data and data processing scripts for a subset of the LINCS Drug Repurposing Project. In this project, we perturbed A549 cells with ~1,500 compounds across 6 doses with ~4 biological replicates.

For a specific list of compounds tested, see metadata.

Image-Based Profiling

We apply a unified, image-based profiling pipeline to all Drug Repurposing Hub Cell Painting plates. We use pycytominer as the primary tool for image-based profiling.

The profiles are processed and stored in the profiles/ directory. See profiles/README.md for more details and for instructions on how to reproduce the pipeline.

For more details about image-based profiling in general, please refer to Caicedo et al. 2017.

Computational Environment

We use conda to manage the computational environment.

After installing conda, execute the following to install and navigate to the environment:

# First, install the `lincs` conda environment
conda env create --force --file environment.yml

# Then, activate the environment and you're all set!
conda activate lincs

Also note that when contributing to the repository, make sure to add any new package in the environment.yml file.