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bioRxiv · 10.1101/2023.08.03.551897

SiCR: Web application for single-cell repertoire analysis and immune profiling

Ishikawa, M.·Matsumoto, K.·Okuzaki, D.
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Abstract

BackgroundSingle-cell RNA sequencing (scRNA-seq) allows analysis of complete sequences of antigen receptors in individual cells. However, it is a complex technique that requires multiple analyses to obtain accurate results. Although several user-friendly tools for scRNA-seq are available, none are specifically designed for immune profiling. ResultsWe developed a web application called SiCR that is based on the Shiny framework of the R package and specializes in single-cell immune profiling. SiCR allows clustering and cell typing required for both general single-cell and immune profiling analyses, such as predicting whether the chronotype is expanding in each group and the antigen the expanding chronotype targets. These analyses can be performed using a cursor control. SiCR also allows for detailed figure settings, enabling immediate publication of results. ConclusionsSiCR is a comprehensive workbench that can be used by biologists for single-cell immune profiling. Currently, it is the only web application that allows single-cell repertoire analysis using both raw and preprocessed data. Moreover, SiCR significantly reduces the time and effort required to analyze and interpret information in single-cell immune profiling. Therefore, SiCR is a potential reference application for interactive analysis and investigation of biological data, especially for immune profiling.

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Ishikawa, M., Matsumoto, K., Okuzaki, D.. 2023-08-06. SiCR: Web application for single-cell repertoire analysis and immune profiling. https://doi.org/10.1101/2023.08.03.551897

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