FAQ

Is this a clinical diagnostic tool?

No. Oncology in Gradient Biotech is a research and translational analysis workspace. Outputs must not be used for clinical diagnosis, treatment selection, or regulatory decision-making. This is not a replacement for expert oncology review.

Do I need R, CellPhoneDB, or maftools installed locally?

No. Upload files through the web UI and the platform handles analysis. Reference implementations inform the underlying algorithms but you never need to run them yourself.

How do I run my first pipeline?

Create a study, upload a MAF or clinical CSV (see Sample data), and run the matching pipeline from its workflow page. See Quick start.

Cell communication failed — what should I check?

Make sure both the expression and metadata files are selected and that they share matching cell_id values, with a cell_type column in the metadata file.

Mutation landscape failed — what should I check?

Confirm your mutation file is selected and is a valid MAF-style CSV with the required columns (Hugo_Symbol, Tumor_Sample_Barcode, Variant_Classification, and position/allele columns).

Survival analysis failed — what should I check?

Confirm your clinical file is selected and has patient_id, time_to_event_days, and event_observed columns.

Interpretation failed — source runs not found

The runs you selected for interpretation must still be complete and available. If one was deleted after you started, re-run the interpretation with currently available runs.

How does oncology relate to Computational Biology?

Computational Biology owns single-cell clustering, spatial transcriptomics, differential expression, and biomarker ML. Oncology adds cell-cell communication, immune deconvolution, mutation landscape, survival analysis, and clinical endpoint integration. TME profiling calls compbio infrastructure rather than duplicating it.

How does oncology relate to Pathology?

Pathology owns whole-slide imaging, tissue segmentation, and spatial quantification. Oncology uses pathology outputs for pathology-integrated spatial TME analysis without rebuilding the image processing layer.