New tool automates cell identification in complex datasets

Osaka, Japan – Analyzing single-cell RNA sequencing (scRNA-seq) data is crucial for understanding complex biological processes and disease development, but identifying individual cell types within these vast datasets has been a significant bottleneck. An international research group led by The University of Osaka has developed a new computational tool, scODIN (Optimized Detection and Inference of Names in scRNA-seq data), to automate and streamline this complex process, paving the way for faster discoveries with high-accuracy classification in biomedicine.

scODIN tackles the challenge of cell type identification by employing a tiered system that allows users to define specific cell subsets at different levels of detail. The tool first identifies major cell clusters automatically, like T cells, B cells, and monocytes. Then, researchers can specify more granular subsets, like regulatory T cells or helper T cells, within those broader categories. This flexible approach accommodates varying levels of resolution depending on the research question. Importantly, scODIN recognizes cells with intermediate phenotypes or transitional states, assigning "double labels" which capture the complexity often missed by traditional methods. Furthermore, it employs a k-nearest neighbor algorithm to recover cell identities affected by dropout events, a common issue in scRNA-seq data where some genes fail to be detected.

The automation and streamlined approach offered by scODIN promises to accelerate biomedical research. By alleviating the laborious manual annotation process, researchers can focus on interpreting the biological meaning of their data and pursue new therapeutic avenues more efficiently. This improved efficiency can lead to faster discoveries, particularly in areas like immunology and cancer research, where understanding cellular heterogeneity is crucial for developing personalized therapies.

"scODIN empowers researchers to easily navigate and analyze complex scRNA-seq datasets," says Dr. James Wing, co-senior author of the study published in The Journal of Immunology. "Its automated and flexible approach not only saves time but also reveals intricate details about cellular populations, opening new doors to understanding disease mechanisms and developing effective treatments."

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The article, “Optimized Detection and Inference of immune cell type Names in scRNA-seq data,” was published in The Journal of Immunology at DOI: https://doi.org/10.1093/jimmun/vkaf183

About The University of Osaka

The University of Osaka was founded in 1931 as one of the seven imperial universities of Japan and is now one of Japan's leading comprehensive universities with a broad disciplinary spectrum. This strength is coupled with a singular drive for innovation that extends throughout the scientific process, from fundamental research to the creation of applied technology with positive economic impacts. Its commitment to innovation has been recognized in Japan and around the world. Now, The University of Osaka is leveraging its role as a Designated National University Corporation selected by the Ministry of Education, Culture, Sports, Science and Technology to contribute to innovation for human welfare, sustainable development of society, and social transformation.

Website: https://resou.osaka-u.ac.jp/en