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.

Interactive viewer
UMAP overview of the T cell atlas
Browse the full atlas interactively, including cell states, gene expression, and donor metadata.
Open interactive viewer
cell2specificity toolkit
Code and software for antigen-specificity inference, including tutorials, models, HLA typing, and pathogen exposure analysis.
View toolkit on Github View analysis code on Github
Data downloads
Download processed atlas resources and source antigen-specificity measurements through ArrayExpress.
Integrated single-cell atlas data Raw BEAM antigen specificity data

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 3.8M T cells across metadata dimensions
Loading atlas summary…
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TCR Motif Matcher
Upload a VDJ CSV → match clonotypes against atlas motifs → infer HLA type & pathogen exposure
✓ live mode
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Drop VDJ CSV here
or browse
Expected columns
Required columns:
IR_VDJ_1_junction_aa, IR_VDJ_1_v_call, IR_VDJ_1_j_call,
IR_VJ_1_junction_aa, IR_VJ_1_v_call, IR_VJ_1_j_call,
donor_id
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Upload a VDJ CSV and click Run analysis
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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