tcR: an R package for T cell receptor repertoire advanced data analysis

Nazarov, Vadim; Pogorelyy, Mikhail V.; Komech, Ekaterina A.; Zvyagin, Ivan V.; Bolotin, Dmitriy A.; Shugay, Mikhail; Chudakov, Dmitriy M.; Lebedev, Yuri B.; Mamedov, Ilgar Z.

doi:10.1186/s12859-015-0613-1

Cited by 208 publications

(186 citation statements)

References 21 publications

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“…Analysis of TCR-β repertoire was performed using the tcR R package (Nazarov et al, 2015). Random Forest machine learning for classification predictions was performed using the randomForestSRC R package (Ishwaran and Kogalur, 2010) as previously described (Twyman-Saint Victor et al, 2015).…”

Section: Methodsmentioning

confidence: 99%

CD40 Stimulation Obviates Innate Sensors and Drives T Cell Immunity in Cancer

2016

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SUMMARY Cancer immunotherapies are more effective in tumors with robust T cell infiltrates, but mechanisms to convert T cell-devoid tumors with active immunosuppression to those capable of recruiting T cells remain incompletely understood. Here, using genetically engineered mouse models of pancreatic ductal adenocarcinoma (PDA), we demonstrate that a single dose of agonistic CD40 antibody with chemotherapy rendered PDA susceptible to T cell-dependent destruction and potentiated durable remissions. CD40 stimulation caused a clonal expansion of T cells in the tumor, but the addition of chemotherapy optimized myeloid activation and T cell function. Although recent data highlights the requirement for innate sensors in cancer immunity, these canonical pathways – including TLRs, inflammasome, and Type I interferon/STING – played no role in mediating the efficacy of CD40/chemotherapy. Thus, CD40 functions as a non-redundant mechanism to convert the tumor microenvironment immunologically. Our data provide a rationale for a newly initiated clinical trial of CD40/chemotherapy in PDA.

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Section: Methodsmentioning

confidence: 99%

CD40 Stimulation Obviates Innate Sensors and Drives T Cell Immunity in Cancer

2016

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“…IgGalaxy has the purpose to provide an easy-to-use interface to IgBlast and IMGT/HighV-QUEST results [12]. Some other programs enable to further analyze or visualize statistics on the whole lymphocyte population, such as ARResT/Interrogate [13], tcR [14], ImmunExplorer [15] or VDJviz [16]. …”

Section: Introductionmentioning

confidence: 99%

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

et al. 2016

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BackgroundThe B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia.Methods and ResultsVidjil is an open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time. Vidjil is implemented in C++, Python and Javascript and licensed under the GPLv3 open-source license. Source code, binaries and a public web server are available at http://www.vidjil.org and at http://bioinfo.lille.inria.fr/vidjil. Using the Vidjil web application consists of four steps: 1. uploading a raw sequence file (typically a FASTQ); 2. running RepSeq analysis software; 3. visualizing the results; 4. annotating the results and saving them for future use. For the end-user, the Vidjil web application needs no specific installation and just requires a connection and a modern web browser. Vidjil is used by labs in hematology or immunology for research and clinical applications.

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“…their DNA sequence, its translation to amino acids and their abundances, is imported from ClonoCalc. The table may be offered in CSV or XLS format, similar to the output format of the MiXCR software.Primary descriptive analyses are performed by wrapping the tcR package [5]. …”

Section: Methodsmentioning

confidence: 99%

ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface

Fähnrich¹,

Krebbel²,

Decker³

et al. 2017

BMC Bioinformatics

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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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1575-2) contains supplementary material, which is available to authorized users.

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tcR: an R package for T cell receptor repertoire advanced data analysis

Cited by 208 publications

References 21 publications

CD40 Stimulation Obviates Innate Sensors and Drives T Cell Immunity in Cancer

CD40 Stimulation Obviates Innate Sensors and Drives T Cell Immunity in Cancer

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface

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