Seurat objects associated with the tonsil cell atlas

In the context of the Human Cell Atlas, we have created a single-cell-driven taxonomy of cell types and states in human tonsils. This repository contains the Seurat objects derived from this effort. In particular, we have datasets for each modality (scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics), as well as cell type-specific datasets. Most importantly, this is the input that we used to create the HCATonsilData package, which allows programmatic access to all this datasets within R.

Version 2 of this repository includes cells from 7 additional donors, which we used as a validation cohort to validate the cell types and states defined in the atlas. In addition, in this version we also provide the Seurat object associated with the spatial transcriptomics data (10X Visium), as well as the fragments files for scATAC-seq and Multiome