PhD project of Andreas Hoek

Since its first application in 2009, single cell RNA sequencing (scRNA-seq) has experienced a steep development. Due to the unprecedented resolution of single cell technology it is widely applicable in many different fields of research, ranging from basic research questions such as analyzing differentiation processes in cells up to highly specific biomedical questions such as tumor cell characterisation. Furthermore, scRNA-seq has undergone many developments in the last decade leading to a variety of different protocols, a massive gain in throughput, sensitivity and significant reduction in cost-per-cell compared to its early stages.

As a consequence, scRNA-seq has a need for tailored bioinformatic software solutions able to tackle the new challenges. These include protocol-specific processing of barcodes and unique molecular identifier (UMI) sequences for up to hundreds of thousands of cells in parallel, detection and characterisation of cellular clusters and appropriate visualizations.

During my thesis, I'm developing WASP - a web-accessible scRNA-seq analysis platform. WASP covers a complete workflow for data based on the ddSeq protocol, from raw reads to cell clustering, differential gene expression detection and visualization. Due to its modular design, the software can easily be employed for data from other protocols. To perform on-premise analysis of sensitive data, WASP can be employed using Docker, Conda or simply as a standalone version for Windows-based systems. Furthermore, users can interactively change parameters during the analysis workflow and download publication-ready visualizations.