TCR Agent
Omi's specialised co-pilot for tcr work
I help you explore T-cell and B-cell receptor repertoires from your single-cell data — clonotypes, expansion, V(D)J usage, public clones, and how they link back to phenotype. No more wrestling with scirpy syntax or dandelion configs.
What I can do for you
I parse 10x V(D)J outputs (filtered_contig_annotations, airr.tsv) and merge them straight into your AnnData or Seurat object — no manual joining headaches.
I quantify clonal expansion, diversity (Shannon, Gini, Chao1), and public vs private clones across samples or conditions, and explain what the numbers actually mean for your biology.
I link TCR/BCR clones to gene expression: which clusters are expanded? Are exhausted CD8s the ones with public clones? I'll show you UMAPs colored by clone size and run differential expression on expanded vs non-expanded cells.
I run repertoire comparisons across patients, timepoints, or treatments, and flag interesting shifts — clonal contraction after therapy, emergence of new dominant clones, shared TCRs with VDJdb hits, you name it.
Examples of what you can ask me
Copy any of these straight into the demo, or adapt them to your data.
- 1"What are the top 10 expanded clonotypes in my CD8 cells?"
- 2"Compare TCR diversity between responders and non-responders."
- 3"Are any of my clones in VDJdb? Match against known specificities."
- 4"Show me a UMAP colored by clone size and overlay the top 5 clones."
- 5"Run differential expression: expanded vs singleton CD8 T cells."
- 6"Which V-J pairings are enriched in tumor vs blood samples?"
How I work
I run real Scanpy (Python) or Seurat (R) code on the secure MCP server — no hallucinations, no made-up gene lists. Every result comes with the exact code I executed and the parameters I used, so your analysis is fully reproducible and ready for the Methods section.
Best for
Immunologists, cancer immunotherapy researchers, vaccine biologists, and anyone working with paired scRNA + V(D)J data who wants real repertoire insight without becoming a scirpy/Immcantation expert.
References
- scirpy (Sturm et al., 2020) – Bioinformatics
- Dandelion (Stephenson et al., 2021) – Nature Medicine
- Immcantation / Change-O (Gupta et al., 2015) – Bioinformatics
- VDJdb (Shugay et al., 2018) – Nucleic Acids Research
- Scanpy (Wolf et al., 2018) – Genome Biology
- Seurat (Hao et al., 2021) – Nature Biotechnology
Try TCR now
Jump into the demo with a starter prompt already loaded. Upload your data, or play with our example dataset first.