ePlatypus: an ecosystem for computational analysis of immunogenomics data

Abstract Motivation The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner. Results Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data an...

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Bibliographic Details
Published in:	Bioinformatics (Oxford, England) Vol. 39; no. 9
Main Authors:	Cotet, Tudor-Stefan, Agrafiotis, Andreas, Kreiner, Victor, Kuhn, Raphael, Shlesinger, Danielle, Manero-Carranza, Marcos, Khodaverdi, Keywan, Kladis, Evgenios, Desideri Perea, Aurora, Maassen-Veeters, Dylan, Glänzer, Wiona, Massery, Solène, Guerci, Lorenzo, Hong, Kai-Lin, Han, Jiami, Stiklioraitis, Kostas, D’Arcy, Vittoria Martinolli, Dizerens, Raphael, Kilchenmann, Samuel, Stalder, Lucas, Nissen, Leon, Vogelsanger, Basil, Anzböck, Stine, Laslo, Daria, Bakker, Sophie, Kondorosy, Melinda, Venerito, Marco, Sanz García, Alejandro, Feller, Isabelle, Oxenius, Annette, Reddy, Sai T, Yermanos, Alexander
Format:	Journal Article
Language:	English
Published:	Oxford University Press 02-09-2023
Subjects:	Applications Note
Online Access:	Get full text
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Summary:	Abstract Motivation The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner. Results Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is an open-source web-based platform and provides programming tutorials and an integrative database that helps elucidate signatures of B and T cell clonal selection. Furthermore, the ecosystem links novel and established bioinformatics pipelines relevant for single-cell immune repertoires and other aspects of computational immunology such as predicting ligand–receptor interactions, structural modeling, simulations, machine learning, graph theory, pseudotime, spatial transcriptomics, and phylogenetics. The ePlatypus ecosystem helps extract deeper insight in computational immunology and immunogenomics and promote open science. Availability and implementation Platypus code used in this manuscript can be found at github.com/alexyermanos/Platypus.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Tudor-Stefan Cotet, Andreas Agrafiotis and Victor Kreiner Equal contribution.
ISSN:	1367-4811 1367-4803 1367-4811
DOI:	10.1093/bioinformatics/btad553