human_disease_schaefer

Human disease dataset annoted in Schaefer et al. 2024 ## Processed AnnData Objects This deposit contains processed AnnData objects (single-cell genomics data) that were processed using the `adata_hf_datasets` Python package. The files are in HDF5 (.h5ad) or Zarr format and contain preprocessed gene expression data along with computed embeddings. ### Available Embeddings (.obsm layers) The AnnData objects contain the following embedding layers: `X_pca`, `X_scvi_fm`, `X_geneformer`, `X_gs10k`, `X_geneformer-v1`, `X_cw-geneformer`. ## Related Resources - **HuggingFace Dataset**: [jo-mengr/human_disease_schaefer_single_no_caption](https://huggingface.co/datasets/jo-mengr/human_disease_schaefer_single_no_caption)- **Raw Data Source**: [Download](https://medical-epigenomics.org/papers/schaefer2024/data/datasets/human_disease/rnaseq._.samples.h5ad) ## Package Information These files were processed using the `adata_hf_datasets` package. For more information about the processing pipeline, please refer to the associated HuggingFace dataset repository.