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


'IMGTStatClonotype' R package installation
IMGT/StatClonotype web tool

A. Launching IMGT/StatClonotype

Whenever you want to launch the tool IMGT/StatClonotype you have first to load the package 'IMGTStatClonotype' by typing into R console:

library(IMGTStatClonotype)# Press ENTER
launch() # Press ENTER

B. Selection of the two sets to be compared

The IMGT/StatClonotype web tool is launched on your default web browser.

Toolinterface fig1

C. Display parameters selection

The CDR3-IMGT length range of IMGT clonotypes (AA) can be selected through the left panel to eliminate outliers from the statistical procedure (by default CDR3-IMGT lengths ≥4 and ≤45)). In the lower part of the panel, users can select parameters for the table and graph results display.

D. Results

Results are provided in eight tabs:

1. IMGT/HighV-QUEST set 1

Toolinterface fig2

2. IMGT/HighV-QUEST set 2

The second tab 'IMGT/HighV-QUEST set 2' displays the same information for set 2.

3. Statistical test results

4. Multiple testing procedures plots

5. Synthesis graph

6. CDR-IMGT lengths

The tab 'CDR-IMGT lengths' displays bar graphs for the nb of IMGT clonotypes (AA) (for IMGT clonotype diversity) or nb of sequences assigned to IMGT clonotypes (AA) (for IMGT clonotype expression) in set 1 and set 2 per CDR1-IMGT, CDR2-IMGT or CDR3-IMGT length.

Bar graphs are interactive:
- For each set, CDR-IMGT length is showed under the mouse cursor with the nb of IMGT clonotypes (AA) or nb of sequences assigned to IMGT clonotypes (AA) shown between brackets.
- Possibility to zoom in by clicking and dragging over the graph area if you are interested by a specific range of CDR-IMGT lengths (double clicking again to zoom out).
- Bar graphs are downloadable in PNG format.

The list of IMGT clonotypes (AA) with selected CDR-IMGT length trough the left panel are displayed in tables bellow the bar graphs for set 1 and set 2 .

Note that: CDR-IMGT lengths (x-axis values) are not necessarily successive in graphs because only lengths found in one or both of compared sets are displayed.

Toolinterface fig6

7. CDR-IMGT AA properties

The tab 'CDR-IMGT AA properties' displays the distribution of the IMGT classes of the 20 common amino acids at a specific CDR-IMGT position in set 1 and set 2.

Variability plots based on 'Shannon entropy', 'Wu-Kabat variability'and 'Simpson index' indexes are generated for set 1 and set 2.

Tables giving values of the selected variability index are displayed at the end of the page for each set.

Results can be obtained for IMGT classes of the 20 common amino acids [12] selected through the left panel: 'Physicochemical', 'Hydropathy', 'Volume', 'Chemical', 'Charge', 'Hydrogen donor or acceptor atoms' and 'Polarity'.

The same information is given for set 2.

Toolinterface fig7

8. V-D-J gene associations

The tab 'V-D-J gene associations' displays heatmaps called also Clustered Image maps (CIMs) to represent V-J, V-D or D-J gene associations in set 1 and set 2.
Under heatmaps, tables crossing the V-J, V-D or D-J gene occurrences in set 1 and set 2 are given.

Toolinterface fig8

E. Exiting IMGT/StatClonotype

Whenever you want to exit the IMGT/StatClonotype tool you can press the button "Exit IMGT/StatClonotype" or close the tab on your web browser and press 'ESC' before closing the R console window.

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 upgrades and versions

Version 1.0.4 (25/01/2021)

Version 1.0.3 (10/02/2018)

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


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  [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).
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  [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).
Wednesday, 12 August 2015
Last updated:
Monday, 25 January 2021
Safa Aouinti, Véronique Giudicelli, Patrice Duroux, Sofia Kossida and Marie-Paule Lefranc
Safa Aouinti, Sofia Kossida and Marie-Paule Lefranc