CellDepot

CellDepot enables organized storage, querying, visualization, and comparative analysis of single-cell RNA sequencing (scRNA-seq) datasets to support cross-study gene expression and cell-type investigations.

Key Features:

• Data management: Uploading and organization of single-cell datasets with metadata indexing for downstream queries.
• Metadata querying: Querying the database by attributes such as species and cell type for targeted dataset selection.
• Relational database with conditional filtering: MySQL-based conditional filtering to perform rapid queries and cross-dataset gene expression comparisons.
• cellxgene VIP integration: Embedding of cellxgene VIP for interactive, scalable per-dataset exploration including visualization of cell composition and gene expression.
• Differential expression analysis support: Identification and inspection of differentially expressed genes across cell types within datasets.
• Visualization tools: Visualization capabilities to present complex scRNA-seq data for interpretation and analysis.

Scientific Applications:

• Cross-study comparison: Compare scRNA-seq datasets from different studies to identify concordant and divergent expression patterns.
• Gene expression profiling: Explore gene expression profiles across cells and datasets to characterize molecular signatures.
• Differential expression analysis: Identify differentially expressed genes among cell types or conditions within datasets.
• Cell composition analysis: Analyze and visualize cell-type composition within single-cell datasets to study biological contexts.

Methodology:

Uses a MySQL relational database with conditional filtering for metadata queries, supports dataset upload and metadata indexing by attributes (e.g., species, cell type), and embeds cellxgene VIP for interactive, scalable per-dataset exploration including visualization and differential expression inspection.