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Allows users to reconstruct the native T-cell receptors (TCR)αβ from single cell RNA-seq data of Ag-specific T cells and to link these with the gene expression profile of individual cells. VDJPuzzle enables analysis about TCR diversity and its relationship with the transcriptional profile of different clones. Moreover, single-cell transcriptome analysis can successfully distinguish Ag-specific T cell populations sorted directly from resting memory cells in peripheral blood and sorted after ex vivo stimulation. Moreover, it has been adapted for B-cell receptor (BCRs) and includes additional features to reliably characterizes somatic hypermutation (SHMs).

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VDJPuzzle classification

VDJPuzzle specifications

Software type:
Restrictions to use:
Computer skills:
Command line interface
Operating system:
TopHat2, Trinity, Ensembl GRCh37, MiGMAP

VDJPuzzle distribution


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VDJPuzzle support



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Kirby Institute for Infection and Immunity, UNSW, Australia; School of Medical Sciences, UNSW, Australia

Funding source(s)

Supported by the National Health and Medical Research Council of Australia (NHMRC, ID1121643, 1113904) and Australian Centre for HIV and HCV Research for funding; the UIPA Postgraduate Award UNSW Australia; an NHMRC Fellowship (No. 1043067, 1130128, 1128416). and by a NSW Health Early-Mid Career Fellowship.

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