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clonotypeR | High throughput analysis of T cell antigen receptor sequences

A software package to identify and analyze antigen receptors from high-throughput sequence libraries. ClonotypeR is designed to process, organize and analyze very large numbers of sequences, in the order of millions, typically produced by Roche 454 or Illumina instruments, and is made of two parts. The first contains shell scripts and reference segment sequences to produce a data file where each line represents the detection of a clonotype in a sequence read. The second part is a R module available from Bioconductor, to load and filter the data, and prepare clonotype abundance tables ready for analysis with third-party tools for differential representation analysis, sample clustering, etc.

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clonotypeR classification

clonotypeR specifications

Unique identifier:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Software type:
Restrictions to use:
Programming languages:
R, Shell (Bash)

clonotypeR distribution


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clonotypeR support


  • Charles Plessy <>


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RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Japan; University Pierre et Marie Curie, UPMC/CNRS UMR7211 - INSERM U959, France; RIKEN Center for Integrative Medical Sciences, Laboratory for Immune Homeostasis, Japan

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