validate-schema

Some additional flexibility for CZI single-cell-curation.

In particular, this repository adds the ability to use different gencode versions for human data: v43 and v44.

This repository depends strongly on single-cell-curation, and just extends it in a minimal way.

Usage

cellarium-schema validate test.h5ad

is identical to

cellxgene-schema validate test.h5ad

But for human data you can additionally specify the gencode version (in [43, 44] where 44 is the current cellxgene-schema default) as

cellarium-schema validate --gencode-version 43 test.h5ad

Similar to the cellxgene-schema tool, you can add human-readable labels based on ontology terms using

cellarium-schema validate --gencode-version 43 --add-labels test_labeled.h5ad test.h5ad