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https://github.com/chanzuckerberg/cellxgene.git
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Marcus Kinsella
78176f9711
Add the `cellxgene schema apply` and `cellxgene schema validate` subcommands. The first takes an h5ad file and a yaml with config information and produces a new h5ad that follows the cellxgene data integration schema. The second takes an h5ad and checks if it follows the schema version written into its metadata. Both are currently marked as "experimental" as the primary intended users are still at CZI.
35 lines
1001 B
YAML
35 lines
1001 B
YAML
fixup_gene_symbols:
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X: log1p
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obs:
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cell_type_ontology_term_id:
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louvain:
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CD4 T cells: CL:00001
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B cells: CL:00002
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CD14+ Monocytes: CL:00003
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NK cells: CL:00004
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CD8 T cells: CL:00005
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FCGR3A+ Monocytes: CL:00006
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Dendritic cells: CL:00007
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Megakaryocytes: CL:00008
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tissue_ontology_term_id: UBERON:12345
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assay_ontology_term_id: EFO:12345
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disease_ontology_term_id: MONDO:12345
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ethnicity_ontology_term_id: HANCESTRO:12345
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development_stage_ontology_term_id: HsapDv:12345
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sex: other
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uns:
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version:
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corpora_schema_version: 1.0.0
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corpora_encoding_version: 0.1.0
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organism_ontology_term_id: NCBITaxon:9606
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title: Test dataset
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contributors:
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- name: Marcus
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institution: CZI
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layer_descriptions:
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X: raw
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project_links:
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- link_url: https://chanzuckerberg.com/
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link_name: CZI
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link_type: SUMMARY
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