VDJPuzzle statistics

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VDJPuzzle specifications

Information


Unique identifier OMICS_11387
Name VDJPuzzle
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
TopHat2, Trinity, Ensembl GRCh37, MiGMAP
Maintained No

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Publications for VDJPuzzle

VDJPuzzle in publications

 (2)
PMCID: 5827521
PMID: 29483513
DOI: 10.1038/s41467-018-03243-7

[…] the data using a gaussian distribution and a log link. the coefficient of determination (r2) was independently calculated using the linear model (lm) function in r for each significant regression., vdjpuzzle was utilized to reconstruct full-length tcrαβ from scrnaseq data35. to identify clonally expanded tcrs, we have considered a clone, a tcr when it was present in more than one cell across […]

PMCID: 5630586
PMID: 28986563
DOI: 10.1038/s41598-017-12989-x

[…] and read length affect the detection and reconstruction of tcrαβ. two recently developed bioinformatics methods for reconstruction of full-length tcrαβ from scrna-seq data were used, tracer and vdjpuzzle. the analysis performed with vdjpuzzle revealed successful tcrαβ reconstruction in 1027 cells (79%) (table ). this result was consistent with the results from tracer, with successful tcrαβ […]


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VDJPuzzle institution(s)
Kirby Institute for Infection and Immunity, UNSW, Australia; School of Medical Sciences, UNSW, Australia
VDJPuzzle 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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