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cellxgene-schema CLI must update validation in X (Matrix Layers) #828

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brianraymor opened this issue Mar 27, 2024 · 0 comments
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5.1 Next minor CELLxGENE schema version after 5.0 curation software dp Data Platform Team work

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brianraymor commented Mar 27, 2024

Design

See X (Matrix Layers).

Assay "raw" required? "raw" location "normalized" required? "normalized" location
Visium Spatial Gene Expression REQUIRED. Values MUST be de-duplicated molecule counts. All non-zero values MUST be positive integers stored as numpy.float32.

If uns['spatial']['is_single'] is False then each cell MUST contain at least one non-zero value.

If uns['spatial']['is_single'] is True then the unfiltered feature-barcode matrix (raw_feature_bc_matrix) MUST be used. See Space Ranger Feature-Barcode Matrices. This matrix MUST contain 4992 rows. If the obs['in_tissue'] value is 1, then the cell MUST contain at least one non-zero value. If any obs['in_tissue'] values are 0, then at least one cell corresponding to a obs['in_tissue'] with a value of 0 MUST contain a non-zero value.
AnnData.raw.X unless no "normalized" is provided, then AnnData.X STRONGLY RECOMMENDED AnnData.X
@brianraymor brianraymor added curation software dp Data Platform Team work 5.1 Next minor CELLxGENE schema version after 5.0 labels Mar 27, 2024
@brianraymor brianraymor changed the title cellxgene-schema must update validation in X (Matrix Layers) cellxgene-schema CLI must update validation in X (Matrix Layers) Mar 27, 2024
@Bento007 Bento007 assigned Bento007 and unassigned Bento007 Apr 29, 2024
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