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

Introduction

'IMGTStatClonotype' R package installation


IMGT/StatClonotype implementation and developments

The IMGT/StatClonotype tool was developed by Safa Aouinti (IMGT, LIGM, Montpellier, France) using R software (version 3.3.0) and Shiny framework [11].
Interactive graphs are generated using ggplot2 [13] with plotly [14] and d3heatmap [15] packages.

This work was granted access to the HPC resources of CINES under the allocation 2014-036029 made by GENCI (Grand Equipement National de Calcul Intensif) and to Très Grand Centre de Calcul (TGCC) of the Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) under the allocation 036029 (2010-2016) made by GENCI (Grand Equipement National de Calcul Intensif).


IMGT/StatClonotype: upgrade and new versions

Version 1.0.2 (03/03/2017)


Version 1.0.1 (03/08/2016)

The tab 'Multiple testing procedures plots' now displays interactive scatter plots and interactive line graphs with:


'IMGTStatClonotype' R package update



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., Li, S., 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). Open access PMID: 24600447
  [11]  Beeley, C. Web application development with R using Shiny. Packt Publishing Ltd, (110 pages). (2013).
  [12]  Pommié, C., Levadoux, S., Sabatier, R., Lefranc, G., Lefranc, MP., IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. Journal of Molecular Recognition, 17: 17-34. (2004). PMID: 14872534
  [13] Wickham, H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. (2009).
  [14] Sievert, C., Parmer C., Hocking, T., Chamberlain, S., Ram, K., Corvellec, M. et al. plotly: Create Interactive Web Graphics via 'plotly.js'. (2016).
  [15]  Cheng, J and Galili, T. d3heatmap: Interactive Heat Maps Using 'htmlwidgets' and 'D3.js'. R package version 0.6.1. (2015).
Created:
Wednesday, 12 August 2015
Last updated:
Friday, 03 March 2017
Authors:
Safa Aouinti safa.aouinti@igh.cnrs.fr, Véronique Giudicelli Veronique.Giudicelli@igh.cnrs.fr, Patrice Duroux Patrice.Duroux@igh.cnrs.fr, Sofia Kossida Sofia.Kossida@igh.cnrs.fr and Marie-Paule Lefranc Marie-Paule.Lefranc@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