Introduction

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.

Publications

  1. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
    Cite this
    Shugay M, Bagaev DV, Turchaninova MA, Bolotin DA, Britanova OV, Putintseva EV, Pogorelyy MV, Nazarov VI, Zvyagin IV, Kirgizova VI, Kirgizov KI, Skorobogatova EV, Chudakov DM, 2015-11-01 - PLoS computational biology

Credits

  1. Mikhail Shugay
    Developer

    Pirogov Russian National Research Medical University, Moscow, Russian Federation

  2. Dmitriy V Bagaev
    Developer

    Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russian Federation

  3. Maria A Turchaninova
    Developer

    Pirogov Russian National Research Medical University, Moscow, Russian Federation

  4. Dmitriy A Bolotin
    Developer

    Pirogov Russian National Research Medical University, Moscow, Russian Federation

  5. Olga V Britanova
    Developer

    Central European Institute of Technology, Masaryk University, Czechia

  6. Ekaterina V Putintseva
    Developer

    Central European Institute of Technology, Masaryk University, Czechia

  7. Mikhail V Pogorelyy
    Developer

    Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russian Federation

  8. Vadim I Nazarov
    Developer

    National Research University Higher School of Economics, Moscow, Russian Federation

  9. Ivan V Zvyagin
    Developer

    Central European Institute of Technology, Masaryk University, Czechia

  10. Vitalina I Kirgizova
    Developer

    Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russian Federation

  11. Kirill I Kirgizov
    Developer

    Russian Children's Hospital, Moscow, Russian Federation

  12. Elena V Skorobogatova
    Developer

    Russian Children's Hospital, Moscow, Russian Federation

  13. Dmitriy M Chudakov
    Investigator

    Central European Institute of Technology, Masaryk University, Czechia

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006588
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionCzechia
Submitted ByDmitriy M Chudakov