🚩 Introduction

Genvert is a package that provides an easy and elegant way for gene identifier conversion in Python.

Main Features:

• Native Python implementation: no dependency on R and no need to configure an R environment.
• Reliable and up-to-date: uses the gene annotation databases officially maintained by Bioconductor under an open-source license.
• No reliance on online services: except for downloading the databases, all functions run locally, quickly, and without having to worry about network connections and firewalls.
• Supports multiple species, chip platforms and gene ID types: up to 16 species and 87 chip platforms are supported. Gene IDs can be converted between entrez ID, accession number, ensembl ID, official symbol, alias symbol, etc. (the specific supported types depend on the species).
• Supports multiple input formats: in addition to converting a list of gene IDs directly, a gene expression matrix in a pandas.DataFrame or an AnnData object can also be accepted as input.
• Automatically and elegantly handles many-to-many mappings: several built-in strategies resolve conflicts and duplications caused by many-to-many mappings between two gene ID types.

📥 Installation

Genvert supports Python version ≥ 3.9.

# Core install, AnnData is NOT installed.
pip install genvert

# If you intend to convert / filter AnnData objects, add the extra:
pip install genvert[anndata]

📖 Documentation

For a detailed user guide and API reference, please see the documentation.

📝 Citation

If you use Genvert in your work, please cite the publication as follows:

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⚖ License

Genvert is provided under the GNU General Public License v3.0.

Genvert uses gene annotation databases provided by the Bioconductor Package Maintainer under Artistic-2.0.

The birth of Genvert is inseparable from the following excellent open-source projects:

• pandas
• numpy
• anndata
• scipy
• requests
• tqdm

The logo of Genvert is modified from the excellent work DNA by Luiz Carvalho under the CC BY 3.0 License.

Open source leads the world to a brighter future.