scNetViz is a Cytoscape app designed to support the biological interpretation of scRNAseq experiments. scNetViz can load expression matrices from:
- EBI's Single Cell Expression Atlas (normalized counts matrix)
- the CZI Human Cell Atlas (from the Matrix service), or
- user provided MatrixMarket files
Category data (clusters, cell type labels, condition, etc.) is loaded from:
- EBI's Single Cell Expression Atlas when the expression matrix is loaded. This includes their clusterings with different *k* values, and all the information in the Experiment design file.
- the CZI Human Cell Atlas (experiment metadata from the Matrix service)
- csv files imported by the user
- calculated clusters (Louvain or Leiden) provided by scNetViz (runs as a service on RBVI servers).
Once loaded, users can perform differential expression analysis between categories (e.g. clusters, cell type, etc.) and create per-cluster protein-protein interaction networks of the most significant expression changes. scNetViz also supports performing enrichment analysis in the networks to find enriched pathways or GO terms.
scNetViz also provides a number of ways to explore the data sets, including violin plots, heatmaps, tSNE plots, UMAP plots, and can also perform louvain or leiden clustering on the data to provide new categories (as mentioned above).
scNetViz development was funded by a grant from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation and the National Resource for Network Biology.