CopepodTCR — copepodTCR 0.3.2 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
  - Task
  - Usage
  - Algorithm
- Installation
  - Requirements
- Usage
  - Quickstart
  - More detailed quickstart
  - Play with the approach using simulated data (Optional)
  - Peptide occurrence search
  - Peptide overlap
  - Pooling and simulation
  - 3D models
  - Results interpretation with a Bayesian mixture model
  - Data simulation with Bayesian mixture model
- Shiny App