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ALgorithm for Pairing alPHA-BETa T cell Receptors ALPHABETR

Implements algorithms for obtaining T cell receptors (TCR) sequence pairs. ALPHABETR determines CDR3A/CDR3B pairs from high-throughput sequencing data from repeated samples of antigen-specific T cell populations. With ALPHABETR, users can determine CDR3A/CDR3B pairs, dual TCR-alpha clones and clones that share CDR3A or CDR3B sequences, and estimate clonal frequencies.

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ALPHABETR forum

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ALPHABETR versioning

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ALPHABETR classification

ALPHABETR specifications

Software type:
Package/Module
Restrictions to use:
None
Output data:
A list of single and dual TCRα clones, each with their estimated frequency within the parent population.
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Input data:
A list of unpaired sequences associated with the sample.
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 3.0
Version:
0.2.1
Requirements:
Rcpp, clue, dplyr, multicool
Source code URL:
https://github.com/edwardslee/alphabetr.git

ALPHABETR support

Documentation

Maintainer

  • Andrew Yates <>

Credits

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Publications

Institution(s)

Institute of Infection, Immunity & Inflammation, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, UK; St Jude Children's Research Hospital, Memphis, TN, USA; Karolinska Institute, CMB, Stockholm, Sweden

Funding source(s)

This study was supported by Arthritis Research UK and the NIH (R01 AI 093870).

Link to literature

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