If multiple rows are highlighted, only the first is treated as theĬhosen experiment for the following actions: In the accession, experiment (SCEA), description (HCA), or organisms column.Ĭlicking a row to highlight it chooses an experiment.
Searching with a term of interest highlights all rows with matching text The resulting experiment browser lists the available datasets along with theirĪccession codes, brief descriptions, numbers of cells, and other information.Ĭlicking a column header sorts by the contents of that column. Icon in the Cytoscape toolbar or use main menu:Įxperiment→From Single Cell Expression Atlas To browse and load an experiment from an online repository: (closing an experiment table merely hides it)Īnd network display Loading an Experiment – show a panel in the main Cytoscape windowįor adjusting network parameters and performing enrichment analyses – show the table for a previously loaded experiment – read in or calculate additional classifications of the cells – load scRNA-seq quantification from file Using the App Manager ( Apps→App Manager). In Cytoscape, the app can be installed from file Using a web browser, search for and select scNetViz as above, andĭownload the jar file. Select the scNetViz app and click Install.Īn alternative approach is to navigate to the You can search for scNetViz directly by name or by any of its tags:Īutomation, integrated analysis, enrichment analysis, To download and install scNetViz, start Cytoscape andīring up the App Manager ( Apps→App Manager).
annotating network nodes with GO terms, pathways, etc.differential expression analysis based on clusterings or otherĬategorizations of the cells in the scRNA-seq datasetĬorresponding to the sets of top differentially expressed genes.ScNetViz works with other Cytoscape apps, namelyĪnd cyPlot, as well as web services hosted by the To explore the data and to develop biological hypotheses. This app enables scientists who may not be experts in scRNA-seq Several ways of plotting the cells and gene expression data are also available. ScNetViz is a Cytoscape app for identifying differentiallyĮxpressed genes from single-cell RNA sequencing dataĪnd displaying networks of the corresponding proteins for further analysis. ScNetViz: Cytoscape networks for scRNA-seq analysis
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