Single cell RNA seq

Single-cell metadata file: scrnaseq_metadata_table

• Objective of the file: single-cell metadata file that contains cell-level metadata, cell type annotations

• Example format: scrnaseq_metadata_table.parquet

• Requirements:

• Named scrnaseq_metadata_table

• In parquet format

• cell_id as primary key

• Contains the mandatory columns in the table below

• File columns & description:

Name	Type	Mandatory	Description
cell_id	str	TRUE	Maps to the linked clinical data file. There can be mutliple bk_sample_id for one patient_id.
patient_id	str	TRUE	Gene name fitting HGNC ontology
sample_id	str	FALSE	TPM count value
cell_type_level_1_major	str	TRUE	Major cell type classification
cell_type_level_2_mid	str	TRUE	Mid-level cell type classification
cell_type_level_3_granular	str	TRUE	Granular cell type classification
UMAP_1		FALSE
UMAP_2		FALSE

Single-cell counts file: scrnaseq_count_table

• Objective of the file: contains raw counts, log-normalized

• Example format: scrnaseq_count_table.parquet

• Requirements:

• Named scrnaseq_count_table

• In parquet format

• cell_id, gene_name as primary keys

• Contains the mandatory columns in the table below

• File columns & description:

Name	Type	Mandatory	Description
cell_id	str	TRUE	Cell identifier
gene_name	str	TRUE	Gene name fitting HGNC ontology
count	pl.Float32	TRUE	Raw count value
count_lognorm	pl.Float32	TRUE	Log-normalized count value

Single-cell sample file: scrnaseq_sample_level_table

• Objective of the file: contains cell type-specific metrics

• Example format: scrnaseq_sample_level_table.parquet

• Requirements:

• Named scrnaseq_sample_level_table

• In parquet format

• sample_id, cell_type_level_2_mid, gene_name as primary keys

• Contains the mandatory columns in the table below

• File columns & description:

Name	Type	Mandatory	Description
sample_id	str	TRUE	Cell identifier
cell_type_level_2_mid	str	TRUE	Mid-level cell type classification
gene_name	str	TRUE	Gene name fitting HGNC ontology
percentage_expressing	pl.Float32	TRUE	Percentage of cells expressing the gene
avg_log_normalized_expression_expressing	pl.Float32	TRUE	Average log expression in expressing cells
avg_log_normalized_expression_all	pl.Float32	TRUE	Average log expression in all cells
total_cells	pl.Int32	TRUE	Total number of cells