CellDepot: A Unified Repository for scRNA-seq Data and Visual Exploration

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Single-cell RNA sequencing (scRNA-seq) generates large, complex datasets.
• Effective tools are needed for data exploration, comparison, and meta-analysis.
• Current platforms may lack integrated visualization and analytical capabilities.

Purpose of the Study:

• To introduce CellDepot, an integrated web application for scRNA-seq data exploration.
• To provide a user-friendly interface with advanced visualization and analytical tools.
• To facilitate data sharing and collaborative research within the single-cell community.

Main Methods:

• Development of a web application with an integrated data management system.
• Implementation of a MySQL database for efficient data querying and filtering.
• Integration of the cellxgene VIP tool for interactive dataset exploration.
• Inclusion of over 20 plotting functions and high-level analysis methods.

Main Results:

• CellDepot hosts over 270 datasets from 8 species and multiple tissues.
• Users can upload, query, and compare scRNA-seq datasets based on various attributes.
• Advanced visualization and analysis enable refined insights into cell composition and gene expression.
• The platform supports efficient exploration of individual datasets and cross-study comparisons.

Conclusions:

• CellDepot promotes large-scale single-cell data sharing and meta-analysis.
• The open-source platform encourages community contribution, broad adoption, and local deployment.
• It empowers scientists with advanced tools for scRNA-seq data exploration and analysis.