Tool interface
Citing IMGT/StatClonotype:
Aouinti S., Giudicelli V., Duroux P., Malouche D., Kossida S., Lefranc M-P. Front. Immunol. 7:339 (2016). doi:10.3389/fimmu.2016.00339 PMID: 27667992 Abstract Full pdf
Aouinti, S., Malouche, D., Giudicelli, V., Kossida, S., Lefranc, M-P. PLoS One, 10(11):e0142353 (2015). doi:10.1371/journal.pone.0142353 PMID: 26540440 Abstract Full pdf
IMGT/StatClonotype version:
1.0.2 (March 3rd 2017)
Introduction

IMGT/StatClonotype installation

IMGT/StatClonotype should be installed following the IMGT/StatClonotype Documentation


Package for users acquainted with R software

IMGT/StatClonotype installation foldersDocumentsLast modified

R package source[   ]IMGTStatClonotype_1.0.2.tar.gz 03-Mar-2017
R package for Linux and Mac[   ]IMGTStatClonotype_1.0.2.tgz 03-Mar-2017
R package for Windows[   ]IMGTStatClonotype_1.0.2.zip 03-Mar-2017
R package manual[TXT]IMGTStatClonotype-manual.pdf 03-Mar-2017


Example files for testing IMGT/StatClonotype

ExamplesFilesLocusDescriptionLast modified

Example 1 [TXT] file 1   MID1.txt TRB CD4- T cells 16-Dec-2015
[TXT]file 2   MID2.txt TRB CD4+ T cells 16-Dec-2015
Example 2 [TXT]file 1    S1.txtIGH Memory IgD+ 16-Dec-2015
[TXT]file 2    S2.txt IGH Memory IgD-16-Dec-2015

MID1.txt, MID2.txt (example 1) and S1.txt, S2.txt (example 2) are from IMGT/HighV-QUEST statistical output, available in the NCBI Sequence Read Archive under the accession code SRX326382 and SRP037774, respectively.


References:

  [1]  Aouinti, S., Malouche, D., Giudicelli, V., Kossida, S., Lefranc, M-P. IMGT/HighV-QUEST statistical significance of IMGT clonotype (AA) diversity per gene for standardized comparisons of next generation sequencing immunoprofiles of immunoglobulins and T cell receptors. PloS ONE, 10(11): e0142353. (2015) Free Article. PMID: 26540440
  [2]  Lefranc, M-P., Giudicelli, V., Duroux, P., Jabado-Michaloud, J., Folch, G., Aouinti, S. et al. IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res. 43(Database issue):D413-22. (2015) Free Article. PMID: 25378316.
  [3]  Alamyar, E., Giudicelli, V., Shuo, L., Duroux, P. and Lefranc, M.-P. IMGT/HighV-QUEST: the IMGT® web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. Immunome Res., 8:1:2. (2012) PMID: 22647994 pdf
  [4]  Alamyar, E., Duroux, P., Lefranc, M.-P. and Giudicelli, V. IMGT tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT HighV-QUEST for NGS. Methods Mol. Biol. 882:569-604. (2012) PMID: 22665256.
  [5]  Li, S., Lefranc, M.-P., Miles, J.J., Alamyar, E., Giudicelli, V., Duroux, P., et al. IMGT/HighV-QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nature Comm,4:2333. (2013) Open access. PMID: 23995877
  [6]  Lefranc, M-P. and Lefranc, G. The T cell receptor FactsBook. Academic Press, London, UK (398 pages), 2001.
  [7]  Lefranc, M-P. and Lefranc, G. The Immunoglobulin FactsBook. Academic Press, London, UK (458 pages), 2001.
  [8]  Giudicelli, V., Chaume, D., Lefranc, M-P. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res. 33(Database issue):D256-61. (2005)
  [9]  Giudicelli, V., and Lefranc M-P. IMGT-ONTOLOGY 2012. Frontiers in Bioinformatics and Computational Biology. Online access. Front. Genet. 3:79 (2012). PMID: 22654892
  [10]  Lefranc, M-P. Immunoglobulin (IG) and T cell receptor genes (TR): IMGT® and the birth and rise of immunoinformatics. Front Immunol. 5:22. (2014) doi: 10.3389/fimmu.2014.00022. Open access PMID: 24600447
  [11]  Beeley, C. et al. (2013) Web application development with R using Shiny. Packt Publishing Ltd, 110 pages.
Created:
Wednesday, 12 August 2015
Last updated:
Friday, 03 March 2017
Author:
Safa Aouinti safa.aouinti@igh.cnrs.fr
Contacts:
Safa Aouinti safa.aouinti@igh.cnrs.fr, Sofia Kossida Sofia.Kossida@igh.cnrs.fr and Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr