Metadata-Version: 2.4
Name: tidytcells
Version: 2.2.1
Summary: Standardise TR/MH data
Author-email: Yuta Nagano <yutanagano51@proton.me>
Maintainer-email: Yuta Nagano <yutanagano51@proton.me>
Project-URL: Homepage, https://tidytcells.readthedocs.io
Project-URL: Documentation, https://tidytcells.readthedocs.io
Project-URL: Repository, https://github.com/yutanagano/tidytcells
Project-URL: Issues, https://github.com/yutanagano/tidytcells/issues
Keywords: immunology,bioinformatics,TCR,TR,MHC,MH,HLA,T cell,IMGT
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Provides-Extra: dev
Requires-Dist: beautifulsoup4; extra == "dev"
Requires-Dist: build; extra == "dev"
Requires-Dist: odfpy; extra == "dev"
Requires-Dist: pandas; extra == "dev"
Requires-Dist: pip; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: requests; extra == "dev"
Requires-Dist: setuptools; extra == "dev"
Requires-Dist: sphinx-book-theme; extra == "dev"
Requires-Dist: tox; extra == "dev"
Requires-Dist: twine; extra == "dev"
Requires-Dist: wheel; extra == "dev"
Provides-Extra: docs
Requires-Dist: sphinx-book-theme; extra == "docs"
Dynamic: license-file

<div align="center">

<img src="https://raw.githubusercontent.com/yutanagano/tidytcells/main/tidytcells.png" width=700>
<br><br>

![Tests](https://github.com/yutanagano/tidytcells/actions/workflows/tests.yaml/badge.svg)
[![Docs](https://readthedocs.org/projects/tidytcells/badge/?version=latest)](https://tidytcells.readthedocs.io)
[![License](https://img.shields.io/badge/license-MIT-blue)](https://github.com/yutanagano/tidytcells?tab=MIT-1-ov-file#readme)
[![DOI](https://img.shields.io/badge/DOI-10.3389/fimmu.2023.1276106-pink)](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1276106)

### Check out the [documentation page](https://tidytcells.readthedocs.io).

</div>

---

`tidytcells` is a lightweight python package that cleans and standardizes T cell receptor (TR), Major Histocompatibility (MH), and Immunoglobulin (IG) data to be [IMGT](https://www.imgt.org/)-compliant.
The main purpose of the package is to solve the problem of parsing and collating together non-standardized TR datasets.
It is often difficult to compile TR data from multiple sources because the formats/nomenclature of how each dataset encodes TR and MH gene names are slightly different, or even inconsistent within themselves.
`tidytcells` can ameliorate this issue by auto-correcting and auto-standardizing your data.

## Installation

```bash
$ pip install tidytcells
```

## Citing tidytcells

Please cite [our manuscript](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1276106).

### BibTex

```bibtex
@ARTICLE{10.3389/fimmu.2023.1276106,
         AUTHOR={Nagano, Yuta  and Chain, Benjamin },
         TITLE={tidytcells: standardizer for TR/MH nomenclature},
         JOURNAL={Frontiers in Immunology},
         VOLUME={14},
         YEAR={2023},
         URL={https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1276106},
         DOI={10.3389/fimmu.2023.1276106},
         ISSN={1664-3224}
}
```
