tsarina
Tsarina selects shared cancer immunotherapy targets for an individual patient or a population HLA panel.
It starts with reusable cancer-testis antigen (CTA), oncogenic-virus, and recurrent-mutation targets. It then combines tumor context, public immunopeptidomics evidence, healthy-tissue safety evidence, and predicted HLA presentation to produce ranked peptide-MHC (pMHC) candidates.
Choose a workflow
| Goal | Entry point | Result |
|---|---|---|
| Prioritize targets for one patient | tsarina personalize or personalized_targets() |
Ranked CTA, viral, and mutant pMHCs for that patient's HLA type and tumor |
| Design an off-the-shelf CTA panel | tsarina panel |
CTA × HLA matrix with evidence tiers and population-coverage estimates |
| Inspect public peptide observations | tsarina hits |
Cancer, healthy-tissue, and restriction evidence for specified peptides |
Start with the documentation guide for inputs, data setup, and the workflow-specific guides.
Install
pip install tsarina
Install the optional peptide-generation and partitioning dependencies for full functionality:
pip install "tsarina[all]"
Quick start
Prioritize targets for a patient:
tsarina personalize \
--hla 'HLA-A*02:01,HLA-A*24:02,HLA-B*07:02' \
--cta 'MAGEA4=142.5,PRAME=87.3' \
--mutations "KRAS G12D" \
--viruses hpv16 \
--output patient-targets.csv
Build the default global CTA × HLA panel:
tsarina panel --format long --output panel.csv
Both workflows can use registered IEDB or CEDAR ligand exports as public immunopeptidomics evidence. See Data and evidence for setup and interpretation.
Target categories
| Category | Candidate source | Tumor-specific context |
|---|---|---|
| CTA | The canonical oncoref CTA set | Tumor RNA expression and reproductive-tissue restriction |
| Viral | Proteomes from nine oncogenic viruses | Virus detected in the tumor |
| Mutant | Nineteen recurrent hotspots across seven driver genes | Matching mutation detected in the tumor |
Oncoref is the single authority for CTA membership, aliases, HPA restriction calls, and proteoform groups. Tsarina adds downstream evidence and scoring without maintaining a second CTA definition library. The exact boundary is documented in CTA ownership and downstream evidence.
How ranking works
Tsarina applies the same high-level sequence across workflows:
- choose candidates from the relevant shared-target sets;
- enforce tumor context and exclude non-target human peptide matches;
- annotate public cancer and healthy-tissue MS observations;
- predict presentation by the requested HLA alleles; and
- rank pMHCs with explicit evidence and safety provenance.
Public MS evidence strengthens a candidate but does not redefine CTA membership. Healthy, direct-ex-vivo observations outside reproductive tissues and thymus are treated as safety evidence.
Documentation
- Documentation guide — workflow selection and shared concepts
- Personalized target selection — patient inputs, prioritization, and output schema
- CTA panel design — automatic selection, evidence tiers, HLA panels, and coverage
- Data and evidence — data registry, observation classification, scoring, and naming
- CTA ownership and downstream evidence — oncoref/Tsarina responsibilities and maintenance
Development
./develop.sh
./format.sh
./lint.sh
./test.sh
1 maintainer
Release files for tsarina 1.29.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| tsarina-1.29.0.tar.gz | 563.2 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| tsarina-1.29.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.1 MB
Release files / tsarina-1.29.0.tar.gz
| Download URL | tsarina-1.29.0.tar.gz |
|---|---|
| Size | 563.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
5d8734b76dc0c2ce40b104e6aaf53c4691aad0542f90bab3fa4fc1564b9ef08d
|
|
BLAKE2b-256 checksum How to use checksums |
1a2e8b666c8b05c0e1e44c52993ed323031f370fa56d48221021cd2a7abd2671
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.12.6
|
Release files / tsarina-1.29.0-py3-none-any.whl
| Download URL | tsarina-1.29.0-py3-none-any.whl |
|---|---|
| Size | 515.3 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
e53e2ad54ca219215e3276a745b17d2374b9966f5f4c7caa75618c9a34eb39e8
|
|
BLAKE2b-256 checksum How to use checksums |
7448f0345ecc8f38bcf4cb58980a852d6a48042781ed12e6c4d33daf10b3ff67
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.12.6
|
