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.