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:
{
"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:
{
"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.
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.