Upload README.md with huggingface_hub

README.md

@@ -0,0 +1,99 @@
+---
+license: cc-by-4.0
+library_name: scvi-tools
+tags:
+- biology
+- genomics
+- single-cell
+- model_cls_name:SCANVI
+- scvi_version:0.20.0
+- anndata_version:0.8.0
+- modality:rna
+- tissue:Bladder
+- 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
+{
+    "labels_key": "cell_ontology_class",
+    "unlabeled_category": "unknown",
+    "layer": null,
+    "batch_key": "donor_assay",
+    "size_factor_key": null,
+    "categorical_covariate_keys": null,
+    "continuous_covariate_keys": null
+}
+```
+
+**model_summary_stats**:
+|     Summary Stat Key     | Value |
+|--------------------------|-------|
+|         n_batch          |   5   |
+|         n_cells          | 24583 |
+| n_extra_categorical_covs |   0   |
+| n_extra_continuous_covs  |   0   |
+|         n_labels         |  16   |
+|       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['_scanvi_latent_qzm']    |
+|    latent_qzv     |    adata.obsm['_scanvi_latent_qzv']    |
+|    minify_type    |  adata.uns['_scvi_adata_minify_type']  |
+| observed_lib_size | adata.obs['_scanvi_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/Bladder_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