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tcR: an R package for T cell receptor repertoire advanced data analysis.
Nazarov, Vadim I; Pogorelyy, Mikhail V; Komech, Ekaterina A; Zvyagin, Ivan V; Bolotin, Dmitry A; Shugay, Mikhail; Chudakov, Dmitry M; Lebedev, Yury B; Mamedov, Ilgar Z.
Afiliación
  • Nazarov VI; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. vdm.nazarov@gmail.com.
  • Pogorelyy MV; National Research University Higher School of Economics, 20 Myasnitskaya Ulitsa, Moscow, 101000, Russia. vdm.nazarov@gmail.com.
  • Komech EA; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. m.pogorely@gmail.com.
  • Zvyagin IV; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. ekomech@gmail.com.
  • Bolotin DA; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. izvyagin@gmail.com.
  • Shugay M; Central European Institute of Technology, Masaryk University, Brno, Czech Republic. izvyagin@gmail.com.
  • Chudakov DM; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. bolotin.dmitriy@gmail.com.
  • Lebedev YB; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. mikhail.shugay@gmail.com.
  • Mamedov IZ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. chudakovdm@mail.ru.
BMC Bioinformatics ; 16: 175, 2015 May 28.
Article en En | MEDLINE | ID: mdl-26017500
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Inmunoglobulinas / Receptores de Antígenos de Linfocitos T / Análisis de Secuencia de ADN / Secuenciación de Nucleótidos de Alto Rendimiento Límite: Humans Idioma: En Revista: BMC Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2015 Tipo del documento: Article País de afiliación: Rusia Pais de publicación: Reino Unido
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Inmunoglobulinas / Receptores de Antígenos de Linfocitos T / Análisis de Secuencia de ADN / Secuenciación de Nucleótidos de Alto Rendimiento Límite: Humans Idioma: En Revista: BMC Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2015 Tipo del documento: Article País de afiliación: Rusia Pais de publicación: Reino Unido