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STOmics / Stereopy

A toolkit of spatial transcriptomic analysis.
MIT License
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Related issues about GEF file #225

Closed ultraypy closed 5 months ago

ultraypy commented 7 months ago

What are the meanings of geneExp, wholeExp, stat, callExp (Opt) and Attributes in the GEF file format documentation ? Thanks!!

UglyRay7 commented 6 months ago

geneExp image In each binX, there are expression and gene two datasets that work together to record the gene expression matrix. expression for (x, y, count) and gene for gene information (offset, row count). They are combined with the same row index.

wholeExp image In exch binX dataset, every position has been recorded, including non-expression ones. It is like a complete matrix.

stat This dataset records the spatial pattern enrichment for genes.

callExp This part is about the expression matrix at cellbin level, which was generated from the cell segmentation result.