title: tcR: an R package for T cell receptor repertoire advanced data analysis.
abstract: BACKGROUND
  The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing.
  
  
  RESULTS
  Here we introduce tcR, a new R package, representing a platform for the advanced analysis of T cell receptor repertoires, which includes diversity measures, shared T cell receptor sequences identification, gene usage statistics computation and other widely used methods. The tool has proven its utility in recent research studies.
  
  
  CONCLUSIONS
  tcR is an R package for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads. The stable version can be directly installed from The Comprehensive R Archive Network ( http://cran.r-project.org/mirrors.html ). The source code and development version are available at tcR GitHub ( http://imminfo.github.io/tcr/ ) along with the full documentation and typical usage examples.
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. vdm.nazarov@gmail.com.|National Research University Higher School of Economics, 20 Myasnitskaya Ulitsa, Moscow, 101000, Russia. vdm.nazarov@gmail.com.
authors.forename: Vadim I
authors.initials: VI
authors.lastname: Nazarov
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. m.pogorely@gmail.com.
authors.forename: Mikhail V
authors.initials: MV
authors.lastname: Pogorelyy
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. ekomech@gmail.com.
authors.forename: Ekaterina A
authors.initials: EA
authors.lastname: Komech
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. izvyagin@gmail.com.|Central European Institute of Technology, Masaryk University, Brno, Czech Republic. izvyagin@gmail.com.
authors.forename: Ivan V
authors.initials: IV
authors.lastname: Zvyagin
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. bolotin.dmitriy@gmail.com.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Bolotin
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. mikhail.shugay@gmail.com.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Shugay
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. chudakovdm@mail.ru.|Central European Institute of Technology, Masaryk University, Brno, Czech Republic. chudakovdm@mail.ru.
authors.forename: Dmitry M
authors.initials: DM
authors.lastname: Chudakov
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. lebedev_yb@ibch.ru.
authors.forename: Yury B
authors.initials: YB
authors.lastname: Lebedev
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. imamedov78@gmail.com.
authors.forename: Ilgar Z
authors.initials: IZ
authors.lastname: Mamedov
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007136:Immunoglobulins / Q000235:genetics*; D011381:Programming Languages; D011948:Receptors, Antigen, T-Cell / Q000235:genetics* / Q000276:immunology*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D007136:Immunoglobulins; D011948:Receptors, Antigen, T-Cell