File formats

MAF / somatic mutation tables

Mutation landscape accepts MAF-style CSV files. Required columns:

Column	Purpose
Hugo_Symbol	Gene name
Tumor_Sample_Barcode	Sample identifier
Variant_Classification	Missense, nonsense, frameshift, splice site, silent, etc.
Chromosome	Chromosome label
Start_Position	Variant start coordinate
Reference_Allele	Reference base
Tumor_Seq_Allele2	Alternate allele

VCF files can be registered as mutation datasets; the pipeline reads MAF-style tabular exports for analysis.

Copy number alterations

Optional CSV for mutation landscape copy number summary:

Column	Required	Purpose
sample_id	Yes	Sample identifier
gene	Yes	Gene symbol
chromosome	No	Chromosome label
alteration	Yes	amplification or deletion

Clinical endpoints

Survival analysis reads clinical CSV files:

Column	Required	Purpose
patient_id	Yes	Patient identifier
time_to_event_days	Yes	Survival or PFS time in days
event_observed	Yes	1 = event, 0 = censored
treatment_arm	No	Treatment group for stratification

Molecular feature matrix

Optional CSV for survival stratification and Cox regression:

Column	Required	Purpose
patient_id	Yes	Join key to clinical table
Feature columns	No	TMB, immune scores, gene signatures, etc.

Longitudinal trajectories

Optional CSV for treatment timepoint analysis:

Column	Required	Purpose
patient_id	Yes	Patient identifier
timepoint	Yes	baseline, on_treatment, response, relapse
feature	Yes	Feature name
value	Yes	Numeric measurement

Per-cell expression (communication)

Column	Required	Purpose
cell_id	Yes	Cell identifier
Gene columns	Yes	Numeric expression values

Cell metadata (communication)

Column	Required	Purpose
cell_id	Yes	Cell identifier
cell_type	Yes	Annotated cell type label
condition	No	Treatment or response group for comparison

Ligand-receptor database (optional)

Custom CSV for cell-cell communication:

Column	Required	Purpose
ligand	Yes	Ligand gene symbol
receptor	Yes	Receptor gene symbol
pathway	No	Signaling pathway label

Bulk expression (immune profile)

Samples-as-rows, genes-as-columns CSV. First column should identify samples.

Repertoire (immune profile)

TCR/BCR clonotype table with clonotype identifiers, CDR3 sequences, and frequency counts. Format follows scirpy-compatible tabular exports.

Artifact outputs

Pipeline results under data/oncology/artifacts/{run_id}/:

Artifact	Contents
result.json	Full pipeline output with summary, tables, and visualization data

Single-cell and spatial omics

10x Genomics, Visium, Xenium, and bulk RNA-seq formats are handled by the Computational Biology area. Oncology links compbio datasets to study samples via shared patient/sample keys.

Whole-slide images

H&E and IHC whole-slide images are handled by the Pathology area. Oncology uses pathology outputs for spatial TME context without duplicating WSI ingestion.