| --- |
| 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:Mammary |
| - 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 | 11375 | |
| | n_extra_categorical_covs | 0 | |
| | n_extra_continuous_covs | 0 | |
| | n_labels | 14 | |
| | 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/c676cd14-97a7-4ea6-ba70-2c7faa1d61d8/Mammary_training_data.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 |
