About Single Cell Browser
Welcome to the Single Cell Browser, a web-based platform for single cell transcriptomics data exploration and visualization.
Current Features
- Fast, interactive UMAP visualization of gene expression across curated single-cell datasets
- A full plotting suite: feature plots, dot plots, violin plots, co-expression, heatmaps, cell-proportion bars, ridge plots, and more
- Cross-dataset comparison tools to line up a gene, metadata, or marker sets side by side
- Marker gene tables with filtering and click-to-plot
- Enrichment analysis: Gene Ontology (GO), KEGG pathways, and GSEA
- Publication-quality figure export (PNG, SVG, and PDF)
Get Started
To begin exploring our datasets, head to the Home page and select a dataset of interest.
Citations & Acknowledgments
The Single Cell Browser relies on several excellent open-source tools and libraries. If you use this platform in your research, please consider citing the relevant tools:
Single-Cell Analysis
Seurat
Used for single-cell RNA sequencing data analysis, clustering, and visualization.
Hao Y, et al. (2024). Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nature Biotechnology. DOI: 10.1038/s41587-023-01767-y
Satija R, et al. (2015). Spatial reconstruction of single-cell gene expression data. Nature Biotechnology. DOI: 10.1038/nbt.3192
Scanpy
Python-based single-cell analysis toolkit.
Wolf FA, et al. (2018). SCANPY: large-scale single-cell gene expression data analysis. Genome Biology. DOI: 10.1186/s13059-017-1382-0
Visualization
UMAP
Uniform Manifold Approximation and Projection for dimension reduction.
McInnes L, et al. (2018). UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction. arXiv. arXiv:1802.03426
Matplotlib
Python plotting library used for generating publication-quality figures.
Hunter JD (2007). Matplotlib: A 2D Graphics Environment. Computing in Science & Engineering. DOI: 10.1109/MCSE.2007.55
Gene Ontology & Enrichment
Gene Ontology
Framework for gene function annotation.
Gene Ontology Consortium (2021). The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Research. DOI: 10.1093/nar/gkaa1113
Web Framework & UI
Flask
Python web framework powering this application.
Grinberg M. Flask Web Development. O'Reilly Media. flask.palletsprojects.com
Data Storage & Processing
NumPy
Fundamental package for scientific computing with Python.
Harris CR, et al. (2020). Array programming with NumPy. Nature. DOI: 10.1038/s41586-020-2649-2
Pandas
Data analysis and manipulation tool.
McKinney W (2010). Data Structures for Statistical Computing in Python. Proceedings of the 9th Python in Science Conference. pandas.pydata.org
Contact Us
If you have any questions, feedback, or would like to contribute a dataset, please use our contact form or email us at singlecellbrowser [AT] gmail [DOT] com.
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