CopepodTCR — copepodTCR 0.5.1 documentation

# CopepodTCR

CopepodTCR (COmbinatorial PEptide POoling Design for TCR specificity) is a Python tool developed for providing peptide pooling schemes for T cell specificity assays. You can access the tool via Python, the command line, or a web application.

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

For installation guidance, visit the Installation page.

Begin with the package by exploring the Quickstart section on the Usage page. For a deeper understanding, we advise the More detailed quickstart section. The Usage page also lists 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
  - 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