ArticleJournal of immunology (Baltimore, Md. : 1950)2017
Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data.
Article in Journal of immunology (Baltimore, Md. : 1950), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Repertoire Sequencing of B Cells Elucidates the Role of UNG and Mismatch Repair Proteins in Somatic Hypermutation in Humans.Frontiers in immunology · 2019Pooled it
- Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis.Journal of translational medicine · 2026Review
- Neonatal CD19Frontiers in immunology · 2026Article
- Innovative Single-Cell Sequencing Techniques for B cell Analysis and Their Implications for Rational HIV-1 Vaccine Design.Current HIV research · 2026Review
- Complement C3d enables cell-mediated immunity capable of distinguishing spontaneously transformed from nontransformed cells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Human IgMInternational journal of molecular sciences · 2023Article
- IgD shapes the pre-immune naïve B cell compartment in humans.Frontiers in immunology · 2023Article
- B-cell receptor repertoire sequencing: Deeper digging into the mechanisms and clinical aspects of immune-mediated diseases.iScience · 2022Review
- Determining immunoglobulin-specific B cell receptor repertoire of murine splenocytes by next-generation sequencing.STAR protocols · 2022Article
- Long-Term Follow-Up of Newborns with 22q11 Deletion Syndrome and Low TRECs.Journal of clinical immunology · 2022Article
- Age-dependent nasal immune responses in non-hospitalized bronchiolitis children.Frontiers in immunology · 2022Article
- NGS-Based B-Cell Receptor Repertoire AnalysisRepertoire analyses in the Context of Inborn Errors of Immunity.Methods in molecular biology (Clifton, N.J.) · 2022Article
- CloneRetriever: An Automated Algorithm to Identify Clonal B and T Cell Gene Rearrangements by Next-Generation Sequencing for the Diagnosis of Lymphoid Malignancies.Clinical chemistry · 2021Article
- Targeting B cells in the pre-phase of systemic autoimmunity globally interferes with autoimmune pathology.iScience · 2021Article
- RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database.Frontiers in immunology · 2021Article
- Article
- Evaluation of Somatic Hypermutation Status in Chronic Lymphocytic Leukemia (CLL) in the Era of Next Generation Sequencing.Frontiers in cell and developmental biology · 2020Review
- Methods for sequence and structural analysis of B and T cell receptor repertoires.Computational and structural biotechnology journal · 2020Review
- Teleost IgDCell reports · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Antigen Receptor Galaxy (ARGalaxy) is a Web-based tool for analyses and visualization of TCR and BCR sequencing data of 13 species. ARGalaxy consists of four parts: the demultiplex tool, the international ImMunoGeneTics information system (IMGT) concatenate tool, the immune repertoire pipeline, and the somatic hypermutation (SHM) and class switch recombination (CSR) pipeline. Together they allow the analysis of all different aspects of the immune repertoire. All pipelines can be run independently or combined, depending on the available data and the question of interest. The demultiplex tool allows data trimming and demultiplexing, whereas with the concatenate tool multiple IMGT/HighV-QUEST output files can be merged into a single file. The immune repertoire pipeline is an extended version of our previously published ImmunoGlobulin Galaxy (IGGalaxy) virtual machine that was developed to visualize V(D)J gene usage. It allows analysis of both BCR and TCR rearrangements, visualizes CDR3 characteristics (length and amino acid usage) and junction characteristics, and calculates the diversity of the immune repertoire. Finally, ARGalaxy includes the newly developed SHM and CSR pipeline to analyze SHM and/or CSR in BCR rearrangements. It analyzes the frequency and patterns of SHM, Ag selection (including BASELINe), clonality (Change-O), and CSR. The functionality of the ARGalaxy tool is illustrated in several clinical examples of patients with primary immunodeficiencies. In conclusion, ARGalaxy is a novel tool for the analysis of the complete immune repertoire, which is applicable to many patient groups with disturbances in the immune repertoire such as autoimmune diseases, allergy, and leukemia, but it can also be used to address basic research questions in repertoire formation and selection.
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