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 specifications

Software type:
Package
Restrictions to use:
None
Programming languages:
R, Shell (Bash)
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
CC Attribution
Version:
clonotypeR version 1.4

clonotypeR support

Maintainer

Credits

Publications

  • clonotypeR--high throughput analysis of T cell antigen receptor sequences.
    Published in: 2015
    DOI: 10.1101/028696

Institution(s)

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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