scNetViz

Single-cell RNASeq analysis in Cytoscape
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.

1.2.0

Works with Cytoscape 3.7

Release Notes

Primarily a bug fix release: 1. Added support for more flexible import of tables from files. User's can now specify the number of header rows and the table browser respects that. 2. Updated some commands to improve the descriptions.

1.1.0

Works with Cytoscape 3.7

Release Notes

Updated to work with the modified HCA DCP1 API. Also fixed access to HCA projects that provided multiple matrices so that each matrix (generally separate tissues) is now a separate entry.

1.0.6

Works with Cytoscape 3.7

Release Notes

Fixed a number of bugs related to the use of scNetViz through automation. Also added new commands to support visualizing plots and performing calculations.

1.0.5

Works with Cytoscape 3.7

Release Notes

Added support for "create all" command that behaves just like the "Create Networks" button except that the experiment must be loaded first

1.0.4

Works with Cytoscape 3.7

Release Notes

Updated to correspond to changes in both CZI HCA and EBI's single cell expression atlas. Also changed coloring of genes in scatterplots to use the log values.

1.0.2

Works with Cytoscape 3.7

Release Notes

Fixed bug with handling of EBI sc-Array Express metadata that resulted in the last cell being ignored.

1.0.1

Works with Cytoscape 3.7


1.0.0

Works with Cytoscape 3.7


CYTOSCAPE 3

Version 1.2.0

Released 1 Apr 2021

Works with Cytoscape 3.7

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