Introduction
A leading US Biotech company required a framework to handle datasets for spatial transcriptomics. This advanced area of single cell sequencing involves obtaining spatial data and gene expression data on a per cell basis. Datasets of this magnitude require a highly efficient framework.
ProCogia were engaged to design and build a framework in R, enabling researchers to study complex cellular mechanisms using next-generation single cell sequencing.
The Challenge
Data quality was a major challenge due to vast amounts of data associated with millions of cells. Computational power was also a barrier when executing complex analyses, which is often the case with large bioinformatics studies. In addition, we needed to optimize analysis pipelines and reduce runtimes to a few hours, often down from 10+ hours.
Procogia’s Approach
- Our team of Bioinformaticians, R Developers, and Data Scientists was led by a Project Manager who collaborated with the client to ensure scientific accuracy, efficient user-friendly code, and timely delivery of this end-to-end project.
- Drawing on our R for Life Sciences expertise, we built a robust computational framework to analyze and visualize spatial transcriptomic data. This will enable the client to commercialize a product that is the next step in single-cell sequencing analysis.
- We designed and implemented the pipeline framework by refactoring an existing code base for efficient and complete execution of complex analysis algorithms. A script-based pipeline was built into a single R package for ease of use and scalability.
- AWS products, including S3 buckets and Amazon Elastic Kubernetes, were used during the testing and hosting of the pipeline framework to overcome computational limitations when dealing with complex single cell data samples.
The Results
- The framework allows for complex data analysis and efficient integration of multi-modal data.
- Memory requirements are reduced, and R Shiny applications accelerate rendering of visualizations.
- Algorithms used in the analysis pipeline are optimized to ensure robust scientific accuracy.
Services Used
Data Consultancy
We provide Data Consultancy to organizations to optimize your investment in people, processes, and technology.
Data Science
Using a blend of mathematics, software tools, business intelligence, and algorithms, we can draw insights and patterns from your raw data, allowing you to make intelligent data-driven decisions.
Bioinformatics
We deliver scientific results that drive clinical and translational research decisions. Our Bioinformatics team has extensive experience designing, optimizing, executing and analyzing pre-clinical and clinical research projects using next-generation sequencing technologies.
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