ArticleBMC bioinformatics2017
ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 19 citations in OpenAlex.
- Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis.Journal of translational medicine · 2026Review
- Innovative Single-Cell Sequencing Techniques for B cell Analysis and Their Implications for Rational HIV-1 Vaccine Design.Current HIV research · 2026Review
- B-cell receptor repertoire sequencing: Deeper digging into the mechanisms and clinical aspects of immune-mediated diseases.iScience · 2022Review
- Article
- Sleep restriction prior to antigen exposure does not alter the T cell receptor repertoire but impairs germinal center formation during a T cell-dependent B cell response in murine spleen.Brain, behavior, & immunity - health · 2021Article
- Article
- PD-L1 Checkpoint Inhibition Narrows the Antigen-Specific T Cell Receptor Repertoire in Chronic Lymphocytic Choriomeningitis Virus Infection.Journal of virology · 2020Article
- Effects of sleep on the splenic milieu in mice and the T cell receptor repertoire recruited into a T cell dependent B cell response.Brain, behavior, & immunity - health · 2020Article
- Article
- Metabolic and Transcriptional Modules Independently Diversify Plasma Cell Lifespan and Function.Cell reports · 2018Article
- Analyzing Immunoglobulin Repertoires.Frontiers in immunology · 2018Review
- Insights From Analysis of Human Antigen-Specific Memory B Cell Repertoires.Frontiers in immunology · 2018Review
- CD154 Costimulation Shifts the Local T-Cell Receptor Repertoire Not Only During Thymic Selection but Also During Peripheral T-Dependent Humoral Immune Responses.Frontiers in immunology · 2018Article
- T Cell Receptor Profiling in Type 1 Diabetes.Current diabetes reports · 2017Review
- VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.BMC bioinformatics · 2017Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and disease. Over the last few years, several algorithms and tools have been developed to support respective analyses of raw sequencing data of the immune repertoire. These tools focus on distinct aspects of the data processing and require a strong bioinformatics background. To facilitate the analysis of T and B cell repertoires by less experienced users, software is needed that combines the most common tools for repertoire analysis.
resultsWe introduce a graphical user interface (GUI) providing a complete analysis pipeline for processing raw NGS data for human and animal TCR and BCR clonotype determination and advanced differential repertoire studies. It provides two applications. ClonoCalc prepares the raw data for downstream analyses. It combines a demultiplexer for barcode splitting and employs MiXCR for paired-end read merging and the extraction of human and animal TCR/BCR sequences. ClonoPlot wraps the R package tcR and further contributes self-developed plots for the descriptive comparative investigation of immune repertoires.
conclusionThis workflow reduces the amount of programming required to perform the respective analyses and supports both communication and training between scientists and technicians, and across scientific disciplines. The Open Source development in Java and R is modular and invites advanced users to extend its functionality. Software and documentation are freely available at https://bitbucket.org/ClonoSuite/clonocalc-plot .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.