Man pages for aertslab/SCopeLoomR
Build .loom files (compatible with SCope) and extract data from .loom files.
| add_annotated_clustering | add_annotated_clustering |
| add_annotation_by_cluster_annotation_mapping_df | add_annotation_by_cluster_annotation_mapping_df |
| add_clustering | add_clustering |
| add_clustering_markers | add_clustering_markers |
| add_col_attr | add_col_attr |
| add_default_embedding | add_default_embedding |
| add_embedding | add_embedding |
| add_embedding_from_dyno | add_embedding_dyno |
| add_fbgn | add_fbgn |
| add_global_attr | add_global_attr |
| add_global_md_annotation | add_global_md_annotation |
| add_global_md_clustering | add_global_md_clustering |
| add_global_md_clustering_kv | add_global_md_clustering_kv |
| add_global_md_embedding | add_global_md_embedding |
| add_global_md_metric | add_global_md_metric |
| add_global_md_regulon_thresholds | add_global_md_regulon_thresholds |
| add_hierarchy | add_hierarchy |
| add_matrix | add_matrix |
| add_regulons | add_regulons |
| add_regulons_AUC | add_regulons_AUC |
| add_row_attr | add_row_attr |
| add_seurat_clustering | add_seurat_clustering |
| append_clustering_update_ca | append_clustering_update_ca |
| build_loom | build_loom |
| check_global_meta_data | check_global_meta_data |
| check_missings | check_missings |
| chunk_points | chunk_points |
| clear_global_meta_data | clear_global_meta_data |
| close_loom | close_loom |
| col_attrs_exists_by_key | col_attrs_exists_by_key |
| compress_gzb64 | open_loom |
| convert_to_loom_v3_spec | convert_to_loom_v3_spec |
| create_cluster_annotation | create_cluster_annotation |
| create_hierarchy | create_hierarchy |
| create_trajectory | create_trajectory |
| create_trajectory_from_dyno | create_trajectory_from_dyno |
| create_trajectory_from_monocle | create_trajectory_from_monocle |
| decompress_gzb64 | open_loom |
| finalize | finalize |
| flush | flush |
| get_all_cluster_markers | get_all_cluster_markers |
| get_cell_annotation | get_cell_annotation |
| get_cell_ids | get_cell_ids |
| get_cell_mask_by_cluster_name | get_cell_mask_by_cluster_name |
| get_cluster_dgem_by_name | get_cluster_dgem_by_name |
| get_cluster_info_by_cluster_name | get_cluster_info_by_cluster_name |
| get_cluster_info_by_id | get_cluster_info_by_id |
| get_clustering_by_id | get_global_md_clustering_by_id |
| get_clustering_idx_by_cluster_name | get_clustering_idx_by_cluster_name |
| get_clusterings | get_clusterings |
| get_clusterings_with_name | get_clusterings_with_name |
| get_cluster_markers | get_cluster_markers |
| get_cluster_names | get_cluster_names |
| get_col_attr_by_key | get_col_attr_by_key |
| get_default_embedding | get_default_embedding |
| get_dgem | get_dgem |
| get_dspace | get_dspace |
| get_dtype | get_dtype |
| get_embedding_by_name | get_embedding_by_name |
| get_embeddings | get_embeddings |
| get_genes | get_genes |
| get_global_attr | get_global_attr |
| get_global_md_clustering_by_id | get_global_md_clustering_by_id |
| get_global_md_clustering_by_name | get_global_md_clustering_by_name |
| get_global_md_clustering_info_by_name | get_global_md_clustering_info_by_name |
| get_global_meta_data | get_global_meta_data |
| get_next_embedding_id | get_next_embedding_id |
| get_regulons | get_regulons |
| get_regulons_AUC | get_regulons_AUC |
| get_regulon_thresholds | get_regulon_thresholds |
| get_row_attr_by_key | get_row_attr_by_key |
| get_seurat_clustering_resolutions | get_seurat_clustering_resolutions |
| global_meta_data_exists | global_meta_data_exists |
| hdf5_utf8_encode | hdf5_utf8_encode |
| hierarchy_exists | hierarchy_exists |
| init_global_md_embeddings | init_global_md_embeddings |
| init_global_meta_data | init_global_meta_data |
| is_base64_encoded | is_base64_encoded |
| is_gzipped | is_gzipped |
| is_json | is_json |
| is_order_conserved | is_order_conserved |
| list_clusterings_names | list_clusterings_names |
| lookup_all_global_attr | lookup_all_global_attr |
| lookup_loom | lookup_loom |
| open_loom | open_loom |
| remove_col_attr | remove_col_attr |
| remove_global_attr | remove_global_attr |
| remove_row_attr | remove_row_attr |
| sce | Input dataset example |
| tSNE_expr | tSNE example |
| update_cluster_descriptions_by_cluster_annotation_mapping_df | update_cluster_descriptions_by_cluster_annotation_mapping_df |
| update_col_attr | update_col_attr |
| update_global_attr | update_global_attr |
| update_global_meta_data | update_global_meta_data |
| update_row_attr | update_row_attr |
