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Table of Contents

Documentation under construction. This is intended to concentrate all the shared tools of the Carpenter-Singh Lab, part of the Broad Institute’s Imaging Platform.

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.

  1. Under development

    • kaljax: High efficiency single cell tracker using CellProfiler features and a Kalman filter, it aims to support both on CPUs and GPUs.
    • smiles: Standardiser of (Chemical) SMILES.

To be integrated

  • copairs: Find pairs and compute metrics between them.

JUMP Information Central

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 general information here, and details on how to make use of it here.

Contributing

See contributing.md for details.