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LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity

Fig 1

The framework of LRT.

(A) The preprocessed scRNA-seq and scTCR-seq data are integrated based on cell barcodes matching. (B) Cell trajectories are first obtained using the Slingshot algorithm. (C) Clonotypes with similar cell cluster composition are grouped using the Dirichlet multinomial mixtures (DMM) model. (D) For each clonotype cluster, the distributional bias of clones along the trajectories is evaluated via permutation tests. The repertoire is characterized in terms of clonal expansion and diversity, the top-ranked clonotypes, and V and J gene usage patterns, among others.

Fig 1

doi: https://doi.org/10.1371/journal.pcbi.1011300.g001