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scvi-tools
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tabula-sapiens-large_intestine-scvi

scvi-tools
biology
genomics
single-cell
model_cls_name:SCVI
scvi_version:1.1.0
anndata_version:0.10.3
modality:rna
tissue:Large_Intestine
annotated:True
Model card Files Community
tabula-sapiens-large_intestine-scvi
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---
license: cc-by-4.0
library_name: scvi-tools
tags:
- biology
- genomics
- single-cell
- model_cls_name:SCVI
- scvi_version:0.20.0
- anndata_version:0.8.0
- modality:rna
- tissue:Large_Intestine
- annotated:True
---

# Description

Tabula sapiens. An across organ dataset of cell-types in human tissues.

# Model properties

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

**model_init_params**:
```json
{
    "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**:
```json
{
    "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          | 11505 |
| n_extra_categorical_covs |   0   |
| n_extra_continuous_covs  |   0   |
|         n_labels         |   6   |
|       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.

<!-- If your model is not uploaded with any data (e.g., minified data) on the Model Hub, then make
sure to provide this field if you want users to be able to access your training data. See the scvi-tools
documentation for details. -->

Training data url: https://zenodo.org/api/files/fd2c61e6-f4cd-4984-ade0-24d26d9adef6/TS_Large_Intestine_filtered.h5ad

# Training code

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

Training code url: https://github.com/scvi-hub-references/tabula_sapiens/main.py

# References

The Tabula Sapiens: A multi-organ, single-cell transcriptomic atlas of humans. The Tabula Sapiens Consortium. Science 2022.05.13; doi: https: //doi.org/10.1126/science.abl4896