All datasets

Pancreas (alpha=0.5)

Human pancreas cells aggregated from single-cell (Dirichlet alpha=0.5)

reference Luecken et al., 2021
homo sapiens Organism
16,382 × 18,771 Dimensions
1.26 GiB Size
log_cp10k Normalization
Source

Description

Human pancreas cells aggregated from single-cell (Dirichlet alpha=0.5)

Preview

An AnnData object with n_obs × n_vars = 16,382 × 18,771 with slots:

obsm: X_pca
varm: pca_loadings
layers: counts , normalized

Data structure

Name Description Type Data type Size
obs
size_factors The size factors created by the normalisation method, if any. vector float32 16382
cell_type Classification of the cell type based on its characteristics and function within the tissue or organism. vector category 16382
batch A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. vector category 16382
var
feature_name A human-readable name for the feature, usually a gene symbol. vector object 18771
hvg Whether or not the feature is considered to be a 'highly variable gene' vector bool 18771
hvg_score A ranking of the features by hvg. vector float64 18771
obsp
knn_connectivities K nearest neighbors connectivities matrix. sparsematrix float32 16382 × 16382
knn_distances K nearest neighbors distance matrix. sparsematrix float64 16382 × 16382
obsm
X_pca The resulting PCA embedding. densematrix float32 16382 × 50
varm
pca_loadings The PCA loadings matrix. densematrix float64 18771 × 50
layers
counts Raw counts sparsematrix float32 16382 × 18771
normalized Normalised expression values sparsematrix float32 16382 × 18771
uns
dataset_description Long description of the dataset. atomic str 1
dataset_id A unique identifier for the dataset. This is different from the `obs.dataset_id` field, which is the identifier for the dataset from which the cell data is derived. atomic str 1
dataset_name A human-readable name for the dataset. atomic str 1
dataset_organism The organism of the sample in the dataset. atomic str 1
dataset_reference Bibtex reference of the paper in which the dataset was published. atomic str 1
dataset_summary Short description of the dataset. atomic str 1
dataset_url Link to the original source of the dataset. atomic str 1
knn Supplementary K nearest neighbors data. dict 3
normalization_id Which normalization was used atomic str 1
pca_variance The PCA variance objects. dict 2

Download & explore

The processed dataset lives on the OpenProblems public S3 bucket, which is world-readable. Download the file directly, or copy its S3 URI to fetch it with your tool of choice.

dataset.h5ad 1.26 GiB
Download
s3://openproblems-data/resources/datasets/openproblems_v1/pancreas/log_cp10k/dataset.h5ad

Used in

Spatial Decomposition

References

  1. Luecken, M. D., Büttner, M., Chaichoompu, K., Danese, A., Interlandi, M., Mueller, M. F., Strobl, D. C., Zappia, L., Dugas, M., Colomé-Tatché, M., & Theis, F. J. (2021). Benchmarking atlas-level data integration in single-cell genomics. Nature Methods, 19(1), 41–50. 10.1038/s41592-021-01336-8 ↗