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+---
+title: CellxGene-VIP next-level scRNA-seq, spatial transcriptomics, and multiome data visualization
+date: '2025-02-13'
+tease: CELLxGENE-VIP is a frontend plugin of CELLxGENE, enabling users to generate multiple QC plots in high-resolution SVG or PNG format.
+  It can also visualize spatial transcriptomics and 10X multiome.
+hide_tease: true
+tags: [tools]
+supporters:
+- elixir
+- denbi
+- unifreiburg
+authors: nilchia
+authors_structured:
+- github: nilchia
+subsites: [global, all, eu]
+main_subsite: eu
+---
+
+# CELLxGENE-VIP; A Major Step for Single-Cell, spatial transcriptomics, and  multiome Data Analysis
+
+CELLxGENE-VIP (Visualization In Plugin) is an extension of the original [CELLxGENE](https://github.com/chanzuckerberg/cellxgene) tool developed by the Chan Zuckerberg Initiative.
+It can efficiently extract deep insights from single-cell RNA sequencing, spatial transcriptomics, and emerging multiome datasets.
+
+This integration enhances the capabilities of high-throughput data exploration and visualization, bridging the gap between computational power and user-friendly analysis.
+While CELLxGENE focuses on fast and interactive visualization of single-cell data, CELLxGENE-VIP goes a step further by integrating interactive processing and customized visual analytics, providing deeper insights into the data.
+
++ It generates a comprehensive set of over eighteen commonly used quality control and analytical plots in high resolution with highly customizable settings.
++ It provides more advanced analytical functions to gain insights into cellular compositions and deep biology, such as marker gene identification, differential gene expression analysis, and gene set enrichment analysis.
++ It pioneers methods to visualize multi-modal data, such as spatial transcriptomics embedding aligned with histological images and the latest 10x Genomic Multiome dataset.
+
+<div align="center">
+Different QC plots by CELLxGENE in no-time!
+
+<img src="static/violin.png" alt="Spatial Transcriptomics Visualization" width="1000">
+<img src="static/heat.png" alt="Spatial Transcriptomics Visualization" width="1000">
+<img src="static/dot.png" alt="Spatial Transcriptomics Visualization" width="1000">
+
+
+Spatial transcriptomics embedding aligned with histological image on one slice!
+
+<img src="static/ST.png" alt="Spatial Transcriptomics Visualization" width="1000">
+
+Multiome data visualization showing the spectral embedding and TSS enrichment score
+<img src="static/multiome.png" alt="Spatial Transcriptomics Visualization" width="1000">
+</div>
+
+## Conclusion
+
+CELLxGENE-VIP helps researchers go beyond visualization, making single-cell analysis more intuitive, reproducible, and insightful.
+Whether you are an experienced programmer or not, with this tool you can generate multiple QC plots fast and dive deep into your data and unlock new discoveries in your research.
+
+[CELLxGENE-VIP Documentation](https://interactivereport.github.io/cellxgene_VIP/tutorial/docs/)
+
+<div align="center">
+Try it out on <strong>Galaxy</strong> today and take your analysis to the next level!
+</div>
+
+<div align="center">
+    <a href="https://usegalaxy.eu/?tool_id=interactive_tool_cellxgene_vip&version=latest">
+      <button type="button" class="btn btn-primary btn-lg">Start CELLxGENE VIP now</button>
+    </a>
+</div>
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