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Troubleshooting & FAQ
Can I use SeuratExplorer with Seurat v3 objects?
Yes. Old objects are updated automatically when loaded. For very old versions (v2 or earlier) you may need UpdateSeuratObject() first.
Is my data uploaded anywhere?
No. When running locally (launchSeuratExplorer()), everything stays on your computer. Data is only uploaded when you run it on a Shiny Server you control.
Can I save my results? Yes. Most plots download as PDF; tables (DEGs, feature summaries, cell metadata, cluster mappings) download as CSV.
What is the difference between the two "Top Expressed Features" methods?
- Find Top Genes by Cell: genes highly expressed in individual cells — good for cell-specific markers.
- Find Top Genes by Accumulated UMI Counts: genes with high accumulated expression across a cluster — good for cluster-level characteristics.
How do I use the color palettes elsewhere?
Use getColors() in your own scripts.
The app opens but "No dimensionality reduction found".
Your object has no reduction matching ReductionKeyWords. Add a umap/tsne/pca reduction, or launch with different keywords, e.g. launchSeuratExplorer(ReductionKeyWords = c("umap")).
A Feature/Violin/Dot/Heatmap/Ridge page is blank. Usually the entered gene is not present in the selected assay, or no cluster is selected. Gene names are case-insensitive but must exist in the chosen assay — check names on the Search Features page.
Uploading a large file fails.
Increase MaxInputFileSize (see Launch Options), or save the object as .qs2 for better compression.
Heatmap / DEG tests error about a missing package.
Install the optional dependencies from Installation (ComplexHeatmap, presto, MAST, limma, DESeq2).
The demo download seems to stall.
raw.githubusercontent.com is not reachable from some networks. Set a mirror with launchSeuratExplorer(DemoDataURL = "..."), or download the file manually. See Demo Data.
I want to clear the cached demo data. See the "Remove the cached file" section in Demo Data.
I found a bug / want a feature. Open an issue at https://github.com/fentouxungui/SeuratExplorer/issues.