• Table of Contents
  • Tools
    • Libraries
    • To be integrated
  • Contributing

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.

Contributing

See contributing.md for details.