stephenra / lincs-cell-painting

Processed Cell Painting Data for the LINCS Drug Repurposing Project

Processed Data for the LINCS Cell Painting Project

The repository stores data and data processing scripts for a subset of the Broad Drug Repurposing Hub collection of compounds.

In this project, the Connectivity Map team perturbed A549 cells with ~1,500 compounds across 6 doses in 5 technical replicates. We refer to this dataset as LINCS Pilot 1.

For a specific list of compounds tested, see metadata. Information about the compounds can be interactively explored in the CLUE Repurposing app. The Morphology Connectivity Hub is the primary source of this dataset.

Image-Based Profiling

We apply a unified, image-based profiling pipeline to all 136 384-well plates from LINCS Pilot 1 . 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.

License

We use a dual license in this repository. We license the source code as BSD 3-Clause, and license the data, results, and figures as CC0 1.0.