Monorepo of the Carpenter-Singh Lab, hosting many of the tools and methods we develop and use.

Tools

Libraries

• broad_babel: Translate gene names to and from broad and JUMP ids, NCBI and other identifiers.
• jump_compound_annotator: Collect compound names and relationships from multiple online databases using their APIs or web requests.
• jump_portrait: Fetch JUMP images from CellPainting’s AWS servers. It also contains some utilities to explore file names.
• jump_rr: Generate browsable databases of perturbation similarities and morphological feature rankings to be explored and queried on a browser.
• trommel: Data-cleaning functions and pipelines to improve the signal of morphological profiles.
• jump_smiles: Standardiser of (Chemical) SMILES.

Tools outside the monorepo

• copairs: Find pairs and compute metrics between them.
• cp_measure: Extract CellProfiler features directly from Python.

JUMP Cell Painting Hub

JUMP Cell Painting is one of our main projects, it is the creation of a data-driven approach to drug discovery based on cellular imaging, image analysis, and high dimensional data analytics You can find most information at the JUMP Cell Painting Hub.

Contributing

See contributing.md for details.