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metadata
license: cc-by-4.0
library_name: scvi-tools
tags:
  - biology
  - genomics
  - single-cell
  - model_cls_name:SCVI
  - scvi_version:1.1.0
  - anndata_version:0.10.3
  - modality:rna
  - tissue:Small_Intestine
  - annotated:True

Description

Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells from 24 organs of 15 normal human subjects.

Model properties

Many model properties are in the model tags. Some more are listed below.

model_init_params:

{
    "n_hidden": 128,
    "n_latent": 20,
    "n_layers": 3,
    "dropout_rate": 0.05,
    "dispersion": "gene",
    "gene_likelihood": "nb",
    "latent_distribution": "normal",
    "use_batch_norm": "none",
    "use_layer_norm": "both",
    "encode_covariates": true
}

model_setup_anndata_args:

{
    "layer": null,
    "batch_key": "donor_assay",
    "labels_key": "cell_ontology_class",
    "size_factor_key": null,
    "categorical_covariate_keys": null,
    "continuous_covariate_keys": null
}

model_summary_stats:

Summary Stat Key Value
n_batch 2
n_cells 10458
n_extra_categorical_covs 0
n_extra_continuous_covs 0
n_labels 16
n_latent_qzm 20
n_latent_qzv 20
n_vars 4000

model_data_registry:

Registry Key scvi-tools Location
X adata.X
batch adata.obs['_scvi_batch']
labels adata.obs['_scvi_labels']
latent_qzm adata.obsm['_scvi_latent_qzm']
latent_qzv adata.obsm['_scvi_latent_qzv']
minify_type adata.uns['_scvi_adata_minify_type']
observed_lib_size adata.obs['_scvi_observed_lib_size']

model_parent_module: scvi.model

data_is_minified: True

Training data

This is an optional link to where the training data is stored if it is too large to host on the huggingface Model hub.

Training data url: https://zenodo.org/records/7608635/files/Small_Intestine_training_data.h5ad

Training code

This is an optional link to the code used to train the model.

Training code url: N/A

References

The Tabula Sapiens Consortium. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science, May 2022. doi:10.1126/science.abl4896