openCyto

OpenCyto is a framework to facilitate the automated analysis of flow cytometry data, a field that has seen significant technological advancements but slow adoption of automated methods. This tool is particularly relevant for clinical research in cancer, immunology, and vaccines, where data sets' increasing size and complexity present substantial challenges for traditional data management and analysis approaches.

OpenCyto aims to democratize access to automated flow cytometry analysis by addressing barriers to its widespread adoption, including scalability to large data sets encountered in clinical trials and the integration of domain-specific knowledge through the hierarchical relationships among cell populations. It achieves this by enhancing the core BioConductor flow cytometry infrastructure, allowing for memory-efficient scaling and expert knowledge directly into the analysis pipeline.

The definition of analysis pipelines through a simple text-based CSV file minimizes the need for writing data-specific code, making OpenCyto particularly user-friendly and adaptable to repetitive analyses. This feature is a boon for core facilities that routinely handle large volumes of data.