VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
By M. Shugay, D. Bagaev, M. Turchaninova, D. Bolotin, O. Britanova, E. Putintseva, M. Pogorelyy, V. Nazarov, I. Zvyagin, V. Kirgizova and 3 more. PLoS Comput. Biol., 2015
550 citations recorded by the source corpus.
Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.
Subfields: Immunology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/c5994d9f6ed808f510cb95a3225c9f8ab0d6b460
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In Immunology
In Molecular Biology
- Sepp Hochreiter
- Günter Klambauer
- Michael Widrich
- Dmitriy M. Chudakov
- Thomas Unterthiner
- Esben Jannik Bjerrum
Citations in the corpus
- VDJdb: a curated database of T-cell receptor sequences with known antigen specificity (2017, methodology): “A standalone VDJdb annotation tool [https://github.com/antigenomics/vdjdb-standalone] was developed using the VDJtools framework (12).”
- Regulatory T cells exhibit distinct features in human breast cancer (2016, unknown): “Comparative analysis of TCR repertoires of peripheral blood and tumoral Treg and CD4+ T cells was performed to determine their overlaps within individual patients using VDJtools software (Shugay et al., 2015).”
- Modern Hopfield Networks and Attention for Immune Repertoire Classification (2020, methodology): “Immunosequencing data have been analyzed with computational methods for a variety of different tasks (Greiff et al., 2015; Shugay et al., 2015; Miho et al., 2018; Yaari & Kleinstein, 2015; Wardemann & Busse, 2017).”