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IRProfiler – a software toolbox for high throughput immune receptor profiling

Christos Maramis, Athanasios Gkoufas, Anna Vardi, Evangelia Stalika, Kostas Stamatopoulos, Anastasia Hatzidimitriou, Nicos Maglaveras, Ioanna Chouvarda
2018 BMC Bioinformatics  
Results: This work introduces Immune Repertoire Profiler (IRProfiler), a novel software pipeline that delivers a number of core receptor repertoire quantification and comparison functionalities on high-throughput  ...  In the era of high-throughput sequencing (HTS), the abundance of immunogenetic data has revealed unprecedented opportunities for the thorough profiling of T-cell receptors (TR) and B-cell receptors (BcR  ...  The present study introduces a novel software pipeline for immune repertoire profiling of high-throughput TR and BcR sequencing data, called Immunogenetic Repertoire Profiler or IRProfiler.  ... 
doi:10.1186/s12859-018-2144-z pmid:29669518 pmcid:PMC5907363 fatcat:giqdpgrf7zbopmotimnvzp6rfe

TRIP - T cell receptor/immunoglobulin profiler

Maria Th. Kotouza, on behalf of the Hellenic Precision Medicine Network in Oncology, Katerina Gemenetzi, Chrysi Galigalidou, Elisavet Vlachonikola, Nikolaos Pechlivanis, Andreas Agathangelidis, Raphael Sandaltzopoulos, Pericles A. Mitkas, Kostas Stamatopoulos, Anastasia Chatzidimitriou, Fotis E. Psomopoulos
2020 BMC Bioinformatics  
The T cell Receptor/Immunoglobulin Profiler (TRIP) tool offers the opportunity for an in-depth analysis based on the processing of the output files of the IMGT/HighV-Quest tool, a standard in NGS immunoprofiling  ...  Conclusions TRIP is a software framework that provides analytical services on antigen receptor gene sequence data.  ...  Another software toolbox for high throughput immune receptor profiling is available on the Galaxy platform [14] , namely the Immune Receptor Profiler (IRProfiler).  ... 
doi:10.1186/s12859-020-03669-1 pmid:32993478 pmcid:PMC7525938 fatcat:66twsnm2njh4jpgx5d52at7jzm

The Pipeline Repertoire for Ig-Seq Analysis

Laura López-Santibáñez-Jácome, S. Eréndira Avendaño-Vázquez, Carlos Fabián Flores-Jasso
2019 Frontiers in Immunology  
of antibody repertoires so that the reader better decides a strategic approach for the experimental design, and computational pathways for the analyses of immune repertoires.  ...  With the advent of high-throughput sequencing of immunoglobulin genes (Ig-Seq), the understanding of antibody repertoires and their dynamics among individuals and populations has become an exciting area  ...  Maramis C, Gkoufas A, Vardi A, Stalika E, Stamatopoulos K, Hatzidimitriou A, et al. IRProfiler - a software toolbox for high throughput immune receptor profiling.  ... 
doi:10.3389/fimmu.2019.00899 pmid:31114573 pmcid:PMC6503734 fatcat:gkzwlvt235hlrhvwlfcdsspwwi

Ανοσογενετική ανάλυση του ρεπερτορίου του Τ κυτταρικού υποδοχέα των κυτταροτοξικών Τ λεμφοκυττάρων με αλληλούχηση υψηλής απόδοσης

Ευαγγελία Α. Σταλίκα
In the era of high throughput sequencing, our perceptions about immune responses will be revised.  ...  In order to overcome these limitations and obtain insight into the role of antigenic drive in T-LGL lymphoproliferations, we here exploited high-throughput next generation sequencing (NGS) to interrogate  ...  IRProfilerA Software Toolbox for High Throughput Immune Receptor Profiling. 2018;1–11. 93. Thomas N, Heather J, Ndifon W, Shawe-Taylor J, Chain B.  ... 
doi:10.26262/ fatcat:34uykofx6jgutcrkl36sgzwspm