Description
Run totalVI integration followed by neighbour calculations, leiden clustering and run umap on the result.
Name | Type & Properties |
---|---|
--id | string required |
--input | file required |
--layer | string |
--modality | string |
--prot_modality | string |
--reference -r | file required |
Name | Type & Properties |
---|---|
--output | file required output |
--reference_model_path | file output |
--query_model_path | file output |
Name | Type & Properties |
---|---|
--obs_batch | string |
--max_epochs | integer |
--max_query_epochs | integer |
--weight_decay | double |
--force_retrain | boolean_true |
--var_input | string |
Name | Type & Properties |
---|---|
--rna_reference_modality | string |
--rna_obsm_output | string |
Name | Type & Properties |
---|---|
--prot_reference_modality | string |
--prot_obsm_output | string |
Name | Type & Properties |
---|---|
--rna_uns_neighbors | string |
--rna_obsp_neighbor_distances | string |
--rna_obsp_neighbor_connectivities | string |
Name | Type & Properties |
---|---|
--prot_uns_neighbors | string |
--prot_obsp_neighbor_distances | string |
--prot_obsp_neighbor_connectivities | string |
Name | Type & Properties |
---|---|
--rna_obs_cluster | string |
--rna_leiden_resolution | double multiple |
Name | Type & Properties |
---|---|
--prot_obs_cluster | string |
--prot_leiden_resolution | double multiple |
Name | Type & Properties |
---|---|
--obsm_umap | string |