Data upload
Oncology studies combine molecular datasets with clinical cohort metadata, managed from the study Data page.
Samples
Register samples on the study Data page with:
| Field | Purpose |
|---|---|
| External ID | Sample identifier used across pipelines |
| Patient ID | Patient key for clinical endpoint joins |
| Timepoint | Longitudinal position (baseline, on-treatment, relapse) |
| Group label | Cohort comparison group (responder, non-responder, arm A/B) |
| Response status | Clinical response category |
Clinical endpoints
Add survival and outcome records per patient — endpoint type (e.g. overall survival), time to event, and whether the event was observed.
Survival analysis reads this data as a clinical CSV with patient_id, time_to_event_days, and event_observed columns — upload a matching file, or register endpoints individually and export.
Mutation datasets
Upload MAF-style mutation files on the Mutations page. Optional inputs:
| Input | Required | Purpose |
|---|---|---|
| Mutation file | Yes | MAF-style CSV |
| Copy number file | No | Copy number alteration table |
| Panel size (Mb) | No | Sequencing panel size for TMB calculation (default 38.0) |
| Top genes | No | Number of genes in oncoprint (default 20) |
Repertoire datasets
Upload TCR/BCR sequencing files on the Immune page alongside your expression matrix for immune profile analysis.
| Input | Required | Purpose |
|---|---|---|
| Expression file | Yes | Bulk or pseudo-bulk expression matrix |
| Repertoire file | No | TCR/BCR clonotype table |
Expression data for communication and immune pipelines
Cell-cell communication requires per-cell expression and metadata CSV files:
| File | Required columns |
|---|---|
| Expression CSV | cell_id plus gene columns |
| Metadata CSV | cell_id, cell_type; optional condition for comparison |
Immune profile requires a bulk expression matrix CSV with sample rows and gene columns.
Next steps
- File formats — MAF, clinical CSV, expression matrix schemas
- Sample data — examples to test with
- Study workflow