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clonotypeR specifications


Unique identifier OMICS_10237
Name clonotypeR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R, Shell (Bash)
Computer skills Advanced
Version 1.4
Stability Stable
Maintained Yes


No version available


  • person_outline Charles Plessy

Publication for clonotypeR

clonotypeR citations


T follicular helper and T follicular regulatory cells have different TCR specificity

Nat Commun
PMCID: 5413949
PMID: 28429709
DOI: 10.1038/ncomms15067
call_split See protocol

[…] Paired-end 250 bp illumina sequencing data were initially trimmed and subsequently merged using PEAR. clonotypeR toolkit was then used to perform TCR sequence annotation. Two samples had to be discarded due to low sequencing quality (mouse 3 Tfh sample and mouse 4 Tfr sample). Out of the 7,547,998 raw […]


Immune DNA signature of T cell infiltration in breast tumor exomes

Sci Rep
PMCID: 4958917
PMID: 27452728
DOI: 10.1038/srep30064

[…] The reads mapped to the human TCRB region (hg19: chr7:142,000,817–142,510,993) and the unmapped reads were extracted from the BAM files, and converted to fastq using SAMtools and BEDtools. The tools ClonotypeR, MiTCR, and IMSEQ were used to identify rearranged TCR regions from the resulting files. Human TCR references were provided by MiTCR and IMSEQ. We created our own reference for ClonotypeR a […]

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clonotypeR 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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