What Is a Pseudobulk File?¶
A pseudobulk file aggregates gene expression across every spot, pixel, or cell assigned to a given factor, producing one summarized expression profile per factor to represent the spatial-analysis equivalent of a bulk RNA-seq sample.
Where can you download the pseudobulk file?
You can download the pseudobulk file for the active factor layer via the Export button in the Factor Drawer.
Why use pseudobulk files?
- Noise Reduction: Raw transcripts at single pixels or spots are sparse and noisy. Summing them across all units assigned to a factor yields a robust and stable signature.
- Downstream Compatibility: Because it is structured as a standard factor-by-gene expression matrix, the pseudobulk file can be directly used in conventional downstream bulk RNA-seq tools (e.g. DESeq2, GSEA, pathway enrichment).
- Differential Expression: Aggregated profiles drive the statistical tests that generate the marker gene table and Volcano Plot in the Factor Drawer.
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