tutorial arrow
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.


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.

User report

tutorial arrow
Vote up tools and offer feedback
Give value to tools and make your expertise visible

0 user reviews

0 user reviews

No review has been posted.

clonotypeR forum

tutorial arrow
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.

No open topic.

clonotypeR versioning

tutorial arrow
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.

No versioning.

clonotypeR classification

clonotypeR specifications

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

clonotypeR support


  • Charles Plessy <>


tutorial arrow
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.



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

Link to literature

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.