Louise Deconinck
Sessions
anndataR aims to make it easy to work with anndata files in R, either by converting it to a SingleCellExperiment or Seurat object, or by interacting with them directly.
Existing single-cell tools and packages most often live in one of three pre-existing ecosystems. The underlying data structures and on-disk formats differ between these frameworks, making smooth interoperability difficult.
Community-based efforts exist to make this conversion process easier, but they rely on using reticulate and while they can make the conversion process easier, it is far from foolproof: due to the differences between the data structures and philosophies underlying the frameworks, lossless conversion is not possible in all cases.
That is where anndataR comes in: it aims to both make anndata a first-class citizen in R, and to provide conversion functions to and from SingleCellExperiment and Seurat classes. Using anndataR, you can read and write h5ad files in R without using reticulate and access anndata slots.
In order to use the best performing methods for each step of the single-cell analysis process, bioinformaticians need to use multiple ecosystems and programming languages. This is unfortunately not that straightforward. We will give an overview of the different levels of interoperability, and how it is possible to integrate them in a single workflow.
For package developers, making methods accessible is important. We will provide information on how to do this well on the package and method level.