Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes using Mellon

Processed data use in the  the Mellon manuscript

The following scanpy anndata objects are also available

1. preprocessed_t-cell-depleted-bm-rna.h5ad: Anndata object for the RNA modality of the T-cell depleted bone marrow multiome dataset with normalized data, cell type annotations, clusters, pseudo time, fate propensities, MAGIC imputed expression data, cell-state densities, B-cell primed and lineage accessibility scores.
2. preprocessed_t-cell-depleted-bm-atac.h5ad: Anndata object for the RNA modality of the T-cell depleted bone marrow multiome dataset with normalized data, cell type annotations, clusters, cell-state densities, B-cell primed and lineage peaks.
3. preprocessed_t-cell-depleted-bm-rna-metacells.h5ad: Anndata object with metacells for the RNA modality of the T-cell depleted bone marrow multiome dataset .
4. preprocessed_mouse-gastrulation-atlas.h5ad: Anndata object of the preprocessed mouse gastrulation data with normalized data, cell type annotations, clusters, pseudo time, fate propensities, MAGIC imputed expression data,