Introduction

Welcome to the official documentation for danRerLib! danRerLib is a Python package specifically designed for zebrafish researchers interested in genomics and transcriptomics. It is designed to assist with gene ID mapping, ortholog mapping, and functional enrichment analysis using different pathway and functional annotation databases.

Key Features

  • Gene ID Conversion: Easily convert gene IDs between different types, such as NCBI Gene ID, ZFIN ID, Ensembl ID, or Symbol.

  • Orthology Mapping: Perform orthology mapping between zebrafish and human genes.

  • Functional Annotation Retrieval: Explore and retrieve the gene sets for the following databases: the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO) Biological Process (BP), GO Molecular Function (MF), and GO Cellular Component (CC).

  • Enrichment Testing: Conduct functional enrichment analyses to identify statistically significant gene sets or concepts from the KEGG or GO databases.

  • Database Building: Rebuild essential databases for gene and pathway information to ensure you have the most up-to-date data for your research.

Getting Started

If you’re new to danRerLib, we recommend starting with the following resources:

  • Installation Guide: Learn how to install danRerLib on your system.

  • Quick Start Tutorial: Get up and running with danRerLib in just a few minutes.

  • API Reference.: Explore the comprehensive API documentation for detailed information on package functions.

  • Tutorials: Explore comprehensive tutorials for detailed package usage.

Why danRerLib?

  • Ease of Use: danRerLib simplifies gene ID mapping, orthology mapping, and functional enrichment tasks with clear documentation and tutorials specifically for zebrafish researchers.

  • Up-to-Date: We regularly update danRerLib to ensure it aligns with the latest gene and pathway annotation databases.

Contributing

We welcome contributions from the community to improve and enhance danRerLib. If you’re interested in contributing, please review our Contributing Guidelines for more information.

Support and Feedback

If you encounter any issues, have questions, or want to provide feedback, please don’t hesitate to contact us.

License

danRerLib is released under the MIT License. Please review the License for details on how you can use and distribute this package.

Funding

This work was supported by a National Institute of Health (National Institute of Diabetes and Digestive and Kidney Diseases) award [1R21DK134931-01 to Uduak George and Karilyn Sant].