DASH dataset: paired alpha-beta mouse TCRs across 7 epitopes

A dataset of 1924 paired alpha-beta T-cell receptors from mice responding to 7 viral epitopes, collected from 78 subjects. This is the benchmark dataset from Dash et al. (2017) and is widely used for evaluating TCR distance metrics.

Usage

dash

Format

A data.frame with 1924 rows and 12 columns:

subject: Subject identifier (e.g., "mouse_subject0050").
epitope: Epitope specificity: F2, M38, M45, m139, NP, PA, or PB1.
count: Clone count (number of cells observed for this clonotype).
va: V-alpha gene with allele (e.g., "TRAV7-3*01").
ja: J-alpha gene with allele (e.g., "TRAJ33*01").
cdr3a: CDR3-alpha amino acid sequence (e.g., "CAVSLDSNYQLIW").
cdr3a_nucseq: CDR3-alpha nucleotide sequence.
vb: V-beta gene with allele (e.g., "TRBV13-1*01").
jb: J-beta gene with allele (e.g., "TRBJ2-3*01").
cdr3b: CDR3-beta amino acid sequence (e.g., "CASSDFDWGGDAETLYF").
cdr3b_nucseq: CDR3-beta nucleotide sequence.
clone_id: Unique clone identifier.

Source

Dash et al. (2017). Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature, 547, 89–93. doi:10.1038/nature22383

Examples

data(dash)
dim(dash)       # 1924 x 12
#> [1] 1924   12
table(dash$epitope)
#> 
#>   F2  M38  M45   NP   PA  PB1 m139 
#>  117  158  291  305  324  642   87