CopepodTCR

CopepodTCR (COmbinatorial PEptide POoling Design for TCR specificity) is a Python package for designing combinatorial peptide-pooling schemes for T cell specificity assays. The tool can be used from Python and through the web application.

For insight into the method and algorithm, see the Introduction page.

For installation guidance, visit the Installation page.

Start with the Quickstart section on the Usage page. For a more detailed workflow, see More detailed quickstart. The Usage page also contains the function reference.

CopepodTCR was developed at CSHL.

CopepodTCR

• COmbinatorial PEptide POoling Design for TCR specificity
  • How to use
  • Algorithm for CPP generation
• Installation
  • Requirements
• Usage
  • Quickstart
  • More detailed quickstart
  • Play with the approach using simulated data (Optional)
• Function reference
  • Reproducibility
  • Peptide occurrence search
  • Peptides generation and assessment
  • Pooling
  • 3D models
  • Results interpretation with a Bayesian mixture model
  • In silico data generation
  • Plotting results
• Shiny App