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scvi-tools
/
heart-cell-atlas-scvi

scvi-tools
biology
genomics
single-cell
model_cls_name:SCVI
scvi_version:1.1.0
anndata_version:0.10.5.post1
modality:rna
tissue:heart
annotated:True
Model card Files Community
heart-cell-atlas-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:1.1.0
- anndata_version:0.10.5.post1
- modality:rna
- tissue:heart
- annotated:True
---

# Description

Combined single cell and single nuclei RNA-Seq data of 485K cardiac cells with annotations.

# Model properties

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

**model_init_params**:
```json
{
    "n_hidden": 128,
    "n_latent": 10,
    "n_layers": 1,
    "dropout_rate": 0.1,
    "dispersion": "gene",
    "gene_likelihood": "zinb",
    "latent_distribution": "normal"
}
```

**model_setup_anndata_args**:
```json
{
    "layer": "counts",
    "batch_key": null,
    "labels_key": null,
    "size_factor_key": null,
    "categorical_covariate_keys": [
        "cell_source",
        "donor"
    ],
    "continuous_covariate_keys": [
        "percent_mito",
        "percent_ribo"
    ]
}
```

**model_summary_stats**:
|     Summary Stat Key     | Value |
|--------------------------|-------|
|         n_batch          |   1   |
|         n_cells          | 18641 |
| n_extra_categorical_covs |   2   |
| n_extra_continuous_covs  |   2   |
|         n_labels         |   1   |
|          n_vars          | 1200  |

**model_data_registry**:
|      Registry Key      |            scvi-tools Location             |
|------------------------|--------------------------------------------|
|           X            |           adata.layers['counts']           |
|         batch          |          adata.obs['_scvi_batch']          |
| extra_categorical_covs | adata.obsm['_scvi_extra_categorical_covs'] |
| extra_continuous_covs  | adata.obsm['_scvi_extra_continuous_covs']  |
|         labels         |         adata.obs['_scvi_labels']          |

**model_parent_module**: scvi.model

**data_is_minified**: False

# 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://www.heartcellatlas.org/#DataSources

# Training code

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

Training code url: N/A

# References

Kazumasa Kanemaru, James Cranley, Daniele Muraro, Antonio M. A. Miranda, Siew Yen Ho, Anna Wilbrey-Clark, Jan Patrick Pett, Krzysztof Polanski, Laura Richardson, Monika Litvinukova, Natsuhiko Kumasaka, Yue Qin, Zuzanna Jablonska, Claudia I. Semprich, Lukas Mach, Monika Dabrowska, Nathan Richoz, Liam Bolt, Lira Mamanova, Rakeshlal Kapuge, Sam N. Barnett, Shani Perera, Carlos Talavera-López, Ilaria Mulas, Krishnaa T. Mahbubani, Liz Tuck, Lu Wang, Margaret M. Huang, Martin Prete, Sophie Pritchard, John Dark, Kourosh Saeb-Parsy, Minal Patel, Menna R. Clatworthy, Norbert Hübner, Rasheda A. Chowdhury, Michela Noseda & Sarah A. Teichmann. Spatially resolved multiomics of human cardiac niches. Nature, July 2023. doi:10.1038/s41586-023-06311-1.