Welcome to the documentation for the Co-Regulation Search Engine (CORESH).
This branch hosts the complete documentation, structured and presented in the format of a Jupyter Book. The documentation provides a detailed guide for users on how to navigate and utilize the CORESH platform to perform co-regulation analyses across various publicly availabe experiments of gene expression analysis. It includes information on input formats, query processes, result interpretation, and additional features such as enriched word analysis and gene set record exploration.
The Co-Regulation Search Engine (CORESH) is a powerful tool designed to analyze co-regulated gene sets across different experiments and species. Users can input gene lists and select the relevant species and experiment databases to uncover relationships between gene expression patterns. CORESH also provides insights into enriched terms and associations within the gene set to facilitate a deeper understanding of the biological context.
This documentation is built using the Jupyter Book framework, making it easy to navigate and understand. The content is divided into multiple sections that guide you through:
- Input Formats: How to input gene lists and select query and database species.
- Search Process: Step-by-step instructions on running co-regulation searches.
- Interpreting Results: Explanation of enriched words, gene set records, and how to understand the provided statistics (e.g., p-values, pctVar).
- Advanced Features: Details on features like record filtering, result expansion, and data exploration via external tools such as Phantasus.