Using data loaders

https://raw.githubusercontent.com/theislab/sfaira/release/resources/images/figure_rtd_data.png

For a high-level overview of data management in sfaira, read The data life cycle first.

Build data repository locally

Build a repository structure

  1. Choose a directory to dedicate to the data base, called root in the following.

  2. Run the sfaira download script (sfaira.data.utils.download_all). Alternatively, you can manually set up a data base by making subfolders for each study.

Note that the automated download is a feature of sfaira but not the core purpose of the package: Sfaira allows you efficiently interact with such a local data repository. Some data sets cannot be automatically downloaded and need you manual intervention, which we report in the download script output.

Use 3rd party repositories

Some organization provide streamlined data objects that can be directly consumed by data zoos such as sfaira. One example for such an organization is the cellxgene data portal. Through these repositories, one can easily build or extend a collection of data sets that can be easily interfaced with sfaira. Data loaders for cellxgene structured data objects will be available soon! Contact us for support of any other repositories.