WELCOME !
to IMGT/StatClonotype

http://www.imgt.org
IMGT®, the international ImMunoGeneTics information system®

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; 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

IMGT/StatClonotype version:: 1.0.4 (January 25th 2021)

Introduction

IMGT/StatClonotype [1], developed by LIGM (Montpellier University, CNRS) and part of IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org) [2] is a standalone IMGT® tool for statistical analysis of sets from IMGT/HighV-QUEST output [3,4], on the Web since June 2016.
IMGT/StatClonotype works only with uploaded files (.txt format) from the IMGT/HighV-QUEST statistical analysis output ('stats_xxx' file available in 'data' directory of the IMGT/HighV-QUEST statistical analysis output where 'xxx' is the batch name and the locus type).
To get these files, you therefore need to launch the IMGT/HighV-QUEST statistical analysis (IMGT/HighV-QUEST Documentation).
IMGT/StatClonotype uses a generic statistical procedure [1] for identifying significant changes in IG and TR differences of proportions of IMGT clonotypes (AA) diversity and expression [5].
It uses the IMGT gene and allele nomenclature [6,7,8] based on IMGT-ONTOLOGY [9] and IMGT standards in immunoinformatics [10].
IMGT/StatClonotype is a tool incorporated in a new R package ('IMGTStatClonotype') to perform pairwise comparison of sets from IMGT/HighV-QUEST output through a user-friendly web interface implemented using Shiny framework [11] in users' own browser.
IMGT/StatClonotype source is distributed under the GNU Lesser General Public License.

IMGT/StatClonotype installation

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

Package for users acquainted with R software

IMGT/StatClonotype installation folders	Files	Last modified

R package source	IMGTStatClonotype_1.0.4.tar.gz	25-Jan-2021
R package manual	IMGTStatClonotype-manual.pdf	25-Jan-2021

Example files for testing IMGT/StatClonotype

Examples	Files	Locus	Description	Last modified

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

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[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:: Monday, 25 January 2021
Author:: Safa Aouinti safa.aouinti@yahoo.fr
Contacts:: Safa Aouinti safa.aouinti@yahoo.fr, Sofia Kossida Sofia.Kossida@igh.cnrs.fr and Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr