User Documentation
1. Overview
The Integrated Visualization Platform for Spatial & Single-Cell Transcriptomics is a web-based tool designed to help researchers visualize, analyze, and download single-cell and spatial transcriptomics data. Our platform supports interactive exploration of gene expression patterns, clustering results, and spatial organization in tissues.
Key Features
- Interactive Data Visualization – Explore UMAP, t-SNE, and spatial maps with gene overlays.
- Multi-Tool Gene Visualization – Compare gene expression using violin plots, heatmaps, and dot plots.
- Data Download – Export processed datasets in multiple formats for further analysis.
- Literature Integration – Link visualizations to relevant publications for easy citation.
2. Data Visualization
2.1 Dimensionality Reduction Plots
- Supported Methods: UMAP, t-SNE
- Color by: Clusters, sample group, metadata (e.g., cell type, condition)
2.2 Gene Expression Visualization
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Plot Types:
- Violin plots – Compare gene expression across clusters
- Heatmaps – Compare gene expression levels across different cell clusters
- Dot plots – Show gene expression frequency vs. average expression
- Spatial gene maps – Overlay gene expression on tissue images
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Visualization Exports:
- High-res images: .png and .svg
3. Data Download
3.1 Available Download Formats
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Processed Data:
- h5ad (AnnData), (Seurat)
- Others
- loom, csv, matrix, fastq...
3.2 How to Download
- Select a dataset and click Download Dataset
4. Literature & Citation
4.1 Linked Publications
- Our dataset is associated with original research articles.
- Click How to Cite to generate a BibTeX citation.
4.2 How to Cite This Platform
If you use our platform in your work, please cite:
5. Support & Contact
Technical Issues: support@cellularis.org
Collaborations: research@yourwebsite.com