COmbinatorial PEptide POoling Design for TCR specificity

T cell receptor (TCR) repertoire diversity enables the antigen-specific immune responses against the vast space of possible pathogens. Identifying TCR-antigen binding pairs from the large TCR repertoire and antigen space is crucial for biomedical research. Here, we introduce copepodTCR, an open-access tool to design and interpret high-throughput experimental TCR specificity assays.

copepodTCR implements a combinatorial peptide pooling scheme for efficient experimental testing of T cell responses against large overlapping peptide libraries, that can be used to identify the specificity of (or "deorphanize") TCRs. The scheme detects experimental errors and, coupled with a hierarchical Bayesian model for unbiased interpretation, identifies the response-eliciting peptide sequence for a TCR of interest out of hundreds of peptides tested using a simple experimental set-up.

Documentation: copepodTCR.readthedocs.

Also you can use copepodTCR app.

Cite as

Kovaleva V. A., et al. "copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling." bioRxiv (2023): 2023-11.

Or use the following BibTeX entry:

@article{
    kovaleva2023copepodtcr,
    title        = {copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling},
    author       = {Kovaleva, Vasilisa A and Pattinson, David J and Barton, Carl and Chapin, Sarah R and Minervina, Anastasia A and Richards, Katherine A and Sant, Andrea J and Thomas, Paul G and Pogorelyy, Mikhail V and Meyer, Hannah V},
    year         = 2023,
    journal      = {bioRxiv},
    publisher    = {Cold Spring Harbor Laboratory},
    pages        = {2023--11}
}

Installation

Can be installed with pip:

pip install copepodTCR

or conda:

conda install -c vasilisa.kovaleva copepodTCR

Then you need to install manifold3d, required for 3D modeling of masks. You can skip this step, if you don't plan to print masks for pooling step.

pip install manifold3d

Alternative to manifold3d is Blender, it can be installed from Blender official website (version 4.5 and higher).

You can use :func:cpp.pick_engine() to check with engines are available in you environment.

Requirements

Required packages should be installed simulataneously with the copepodTCR packages.

But if they were not, here is the list of requirements:

    pip install "pandas>=1.5.3"
    pip install "numpy>=1.23.5"
    pip install "trimesh>=3.23.5"
    pip install "pymc>=5.9.2"
    pip install "arviz>=0.16.1"
    pip install "matplotlib>=3.10.5"
    pip install "seaborn>=0.13.2"
    pip install "plotly>=6.2.0"