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Statistical Analysis and Comprehension of the Human Cell Atlas in R / Bioconductor: Access and Scalable Infrastructure

Focus Bioconductor

Project Goal

To produce Bioconductor packages that combine familiar annotation for signatures and cell types with formally curated ontological vocabulary for data aggregation, statistical modeling, and visualization.

Results & Resources

The Carey lab produced a number of Bioconductor packages for single-cell analysis. The ontoProc package provides users with facilities to import and visualize open biomedical ontologies, to relate ontology content to data structures representing cell type expression signatures, and to extend ontological annotation of cell types and states with information about new experimental results. The ctmarks app provides a globally accessible interface to ontoPro utilities. Finally, they created restfulSE and rhdf5client to handle cloud-scale genomic repositories.


Lead Investigator

Vincent Carey
Vincent Carey