Single-cell atlas T cell immunity 2026

A pan-infection single-cell atlas of human T cells unlocks systematic antigen-specificity inference

3.8M+T cells
14pathogens
1,135donors
25datasets
10tissues

Dratva LM, Yu Y, Vlasova EK, Im MG, Polanski K, Alexandrov M, Milchsack LM, Kapuge R, Predeus AV, Shugay M, Kretschmer L & Teichmann SA. (2026)

Data & resources

All datasets, code, and interactive visualisations associated with this work.

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GitHub repository
cell2specificity toolkit — full source code covering tutorials, bundled CellTypist models, HLA and pathogen exposure inference.
github.com/lisadratva/cell2specificity ↗
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Integrated data
Integrated h5ad object covering all 25 datasets, including harmonised metadata and TCR sequences.
coming soon — anndata Collection
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CELLxGENE explorer
Browse the full atlas interactively — cell states, gene expression, and donor metadata.
link coming soon

Interactive tools

Explore the atlas, run cell2specificity analyses in your browser, or inspect TCR–pMHC structures from TCRdock predictions.

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Atlas Explorer
Interactive visualisation of 1.5M clonotypes across metadata dimensions
loading…
Loading atlas summary…
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TCR Motif Matcher
Upload a VDJ CSV → match clonotypes against atlas motifs → infer HLA type & pathogen exposure
⚡ example results
ℹ Live custom repertoire analysis is temporarily disabled; currently showing example results from the Pan-Infection Atlas. Upload your VDJ CSV and click Run Analysis to see the example output.
⚠ Demo mode: the cell2specificity backend is not running in this static deployment. Results below use synthetic example data from three representative donors.
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Drop VDJ CSV here
or browse
Expected columns
The CSV should contain VDJ annotation columns such as:
v_gene, j_gene, cdr3 (and optionally donor, chain). Output from 10x Genomics, TRUST4, or the cell2specificity.tcr_motifs preprocessor all work.
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Upload a VDJ CSV and click Run analysis
Example results will appear here
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TCR–pMHC Structure Viewer
Inspect AlphaFold / TCRdock predicted structures — coloured by pLDDT confidence
3Dmol.js
Representation
Colour by
Options
pLDDT confidence
3065100
Low—High
Load structure
Accepts .pdb with pLDDT in B-factor column (e.g. from TCRdock or processed with write_pdb_with_bfactor_from_plddt).
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Loading demo structure…
TCR–pMHC · GILGFVFTL / HLA-A*02:01 (TCRdock)
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