Metadata-Version: 2.4
Name: gene-jar
Version: 0.1.0
Summary: Resource for harmonizing ambiguous gene symbols
Author-email: Anastasia Bratulin <anastasia.bratulin@nationwidechildrens.org>
License-Expression: MIT
Project-URL: Homepage, https://github.com/cancervariants/gene-jar
Project-URL: Documentation, https://github.com/cancervariants/gene-jar
Project-URL: Changelog, https://github.com/cancervariants/gene-jar/releases
Project-URL: Source, https://github.com/cancervariants/gene-jar
Project-URL: Bug Tracker, https://github.com/cancervariants/gene-jar/issues
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: tables
Requires-Dist: pandas
Provides-Extra: tests
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Provides-Extra: dev
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Dynamic: license-file

# gene-jar

[![image](https://img.shields.io/pypi/v/gene-jar.svg)](https://pypi.python.org/pypi/gene-jar)
[![image](https://img.shields.io/pypi/l/gene-jar.svg)](https://pypi.python.org/pypi/gene-jar)
[![image](https://img.shields.io/pypi/pyversions/gene-jar.svg)](https://pypi.python.org/pypi/gene-jar)

[![Actions status](https://github.com/cancervariants/gene-jar/actions/workflows/checks.yaml/badge.svg)](https://github.com/cancervariants/gene-jar/actions/checks.yaml)

<!-- description -->
This resource is useful for resolving ambiguous gene symbols powered by thousands of annotations characterizing the relationships between genes and their symbols. Please see the [quickstart notebook](gene_jar_example_use.ipynb) for example usage.

Given a gene symbol, this package:
- finds all genes with this symbol as an alias or primary gene symbol
- provides relationships between the gene symbols and their genes, when available
- provides more detailed information when given the relationship type with the gene symbol

Relationship rank was determined using a test set of ambiguous gene symbols and the highest accurate resolution rate. See [gene jar analysis repo](https://github.com/cancervariants/gene-jar-analysis/tree/09ecaf9fdae49915a6fd35a6830b46c6ae182e2a/analysis/gene_ids_in_lit)

Resources used for annotations include:
[Ensembl](https://www.ensembl.org/index.html)
[HGNC](https://www.genenames.org/)
[NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/)
[Saccharomyces Genome Database](http://sgd-archive.yeastgenome.org/)
[FLJ Human cDNA Database](https://flj.lifesciencedb.jp/top/sys_info/02_about_database/accession_no/download_v032.html)
[OMIM](https://omim.org/downloads/)
[Uniprot](https://www.uniprot.org/)
[Mouse Genome Informatics](https://www.informatics.jax.org/)
<!-- /description -->

---

## Installation

Install from [PyPI](https://pypi.org/project/gene-jar/):

```shell
python3 -m pip install gene-jar
```

---

## Feedback and contributing

We welcome bug reports, feature requests, and code contributions from users and interested collaborators. Please make an issue.
