Welcome to tidytcells’s documentation!

Note

This package is currently in the alpha stage of development.

Note

Support for species other than Homo sapiens is currently limited (see Supported species and species strings). Support for more species is planned for the future.

tidytcells is a lightweight Python package written for bioinformaticians who work with T cell receptor (TCR) data. The main purpose of the package is to solve the problem of parsing and collating together non-standardised TCR datasets. It is often difficult to compile TCR data from multiple sources because the formats/nomenclature of how each dataset encodes TCR and MHC gene names are slightly different, or even inconsistent within themselves. tidytcells attempts to ameliorate this issue by providing simple functions that can standardise TCR and MHC gene symbols to their officially accepted versions, as defined by IMGT.

Contents

• Installation
  • Via PyPI (recommended)
  • From source
• Usage
  • Standardising TCR/MHC gene names
  • Other MHC utilities
  • Example usage
  • Supported species and species strings
• API reference
  • tidytcells
• Contribute
  • Setting up a development environment
  • Running tests

Indices and tables

• Index

• Module Index

• Search Page