Data upload

The Immunology workspace currently records dataset metadata and supports pipeline inputs from file paths or inline rows, depending on the analysis.

Dataset modalities

Modality	Use
scrna	Single-cell RNA-seq annotations or expression-derived labels
cite_seq	ADT/protein counts for CITE-seq summaries
vdj	TCR/BCR contig, AIRR, or bulk repertoire tables
spatial	Spatial cell coordinates and immune labels
bulk_rna	Bulk expression tables for immune profiling contexts
atac	Tabular ATAC peak accessibility rows
fcs	CSV/TSV cytometry event tables; binary FCS is gated
cytokine	Cytokine activity or signaling measurements

File path inputs

Analysis endpoints accept file path parameters when the backend can read the file:

• input_path
• path
• expression_path
• metadata_path
• adt_path
• atac_path
• fcs_path

Inline row inputs

Many pipelines accept rows, expression_rows, metadata_rows, adt_rows, atac_rows, or fcs_rows. This is useful for smoke tests, demos, and small tabular datasets.

Upload limitations

The app does not yet provide a full Immunology file-upload manager. Register datasets first, then pass paths or rows through the analysis panels/API until upload workflows are expanded.