A Notebook-Based Analysis Workspace for the Human Cell Atlas

To develop a notebook-based analysis workspace to enable non-programming investigators to take advantage of the Human Cell Atlas resource and collect cell type expression markers for annotation of cell clusters derived from single-cell RNA-seq data.

The Mesirov lab developed and deployed an initial release of their Human Cell Atlas (HCA) notebook workspace and repository. On this site users can create, develop, share and publish notebooks that can query, access, and analyze datasets hosted on the HCA Data Coordination Platform (DCP). The website contains vignettes for various activities, such as computing the number of available cells of a certain cell type in the DCP, and also has an initial collection of notebooks implementing single-cell analysis workflows.