Technical Name Listening to the sea of biological big data (Seashell): an automatic web portal system for single-cell RNA sequencing (scRNA-seq) analysis
Project Operator Academia Sinica
Project Host 林仲彥
Single-cell RNA sequencing (scRNA-seq) is now widely applied to biomedical researches. However, it is also difficult to handle the massive single-cell omics data without basic knowledge. To solve this problem, our research group developed an automatic web portal system for single-cell RNA sequencing analysis.
The web portal system can be divided into two parts. First, users can apply the Galaxy-based docker image for raw data preprocessing. Now the docker image supports the raw data preprocessing of the most popular 10x Genomics data, and more analytic platforms will be added in the coming future. Second, preprocessed data can be uploaded to the RShiny-based web portal to perform custom analysis. The pipeline contains cell quality control, cluster analysis, marker identification, and other popular tools.
In a nutshell, the Seashell platform can help researchers to perform their custom data analysis without programming knowledge, improving the efficiency of scRNA-seq analysis.
Scientific Breakthrough
The characteristics of scRNA-seq analysis platform Seashell contain : (1) the custom pipeline of data analysis from raw data (.fastq) (2) the user-friendly interface of a single-cell database. (3) the integrated visualization platform which contains various tools.
We also applied this web portal system for cluster analysis of cell therapy products and successfully identified the cell sub-populations related to therapeutic efficacy and safety, demonstrating the clinical and industrial application of this platform.
Industrial Applicability
Our research group cooperated with the cell therapy groups in the Taipei Medical University and National Taiwan University College of Medicine, performing data analysis for high dimensional single-cell transcriptomics data of two potential cell products by our Seashell platform. We successfully obtained the safety and therapeutic information of these products and demonstrated the performance of the web portal system. We also plan to apply this web-based platform to various research and industrial fields in the future.
Keyword single-cell RNA sequencing transcriptome docker galaxy droplet-seq cell therapy web application biomarker identification precision medicine big data
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