Man pages for bschilder/scKirby
Automated ingestion and conversion of various single-cell data formats.
| activate_conda | Activate conda environment |
| anndata_to_ctd | Convert: 'AnnData' ==> 'CellTypeDataset' |
| anndata_to_list | Convert: 'AnnData' ==> 'list' |
| anndata_to_se | Convert: 'Anndata' ==> 'SummarizedExperiment' |
| anndata_to_seurat | Convert: 'Anndata' ==> 'Seurat' |
| calc_cor | Compute all pairwise trait correlations |
| cds_to_anndata | Convert: 'CellDataSet' ==> 'AnnData' |
| cds_to_list | Convert: 'CellDataSet' ==> 'list' |
| cds_to_se | Convert: 'CellDataSet' ==> 'SummarizedExperiment' |
| cds_to_seurat | Convert: 'CellDataSet' ==> 'Seurat' |
| class_dict | Class dictionary |
| converters | Converters |
| ctd_to_se | Convert: 'CellTypeDataset' ==> 'SingleCellExperiment' |
| ctd_to_seurat | Convert: 'CellTypeDataSet' ==> 'Seurat' |
| dimreduc_to_list | Convert: 'AnnData' ==> 'list' |
| example_anndata | Example 'anndata' |
| example_obj | Example single-cell data object |
| get_cor | Extract correlation matrix |
| get_graphs | Get graphs |
| get_n_elements | Get N elements |
| get_obs | Get observations metadata |
| get_obsm | Extract reductions |
| get_obs_names | Get obs names |
| get_uns | Get unstructured metadata |
| get_var | Get variable metadata |
| get_variable_features | Get variable features |
| get_varm | Extract variable loadings |
| get_var_names | Get var names |
| get_x | Get data |
| h5seurat_to_anndata | Convert: 'h5Seurat' ==> 'anndata' |
| h5seurat_to_seurat | Convert: 'Seurat' ==> 'H5Seurat' |
| has_graph | Has graph |
| ingest_data | Import and standardize scRNAseq data across different formats |
| is_class | Is class |
| is_installed | Is package installed |
| list_to_anndata | Convert: 'list' ==> 'AnnData' |
| list_to_dimreduc | Convert: list ==> 'DimReducObject' |
| list_to_se | Convert: 'list' ==> 'SummarizedExperiment' |
| list_to_seurat | Convert: 'list' ==> 'Seurat' |
| load_rdata | load RData |
| loom_to_list | Convert: 'loom' ==> 'list' |
| loom_to_scle | Convert: 'loom' ==> 'SingleCellLoomExperiment' |
| loom_to_se | Convert: 'loom' ==> 'SummarizedExperiment' |
| loom_to_seurat | Convert: 'loom' ==> 'Seurat' |
| map_data | Convert single-cell data |
| map_data_anndata | Convert AnnData |
| map_data_h5seurat | Convert h5Seurat |
| map_data_matrix | Convert matrix |
| map_data_se | Convert SummarizedExperiment |
| map_data_seurat | Convert Seurat |
| matrices_to_assayobjects | Matrices to 'AssayObjects' |
| matrix_to_se | Convert: 'matrix' ==> 'SummarizedExperiment' |
| matrix_to_seurat | Convert: 'matrix' ==> 'Seurat' |
| merge_anndata | Merge 'anndata' objects |
| merge_sce | Merge a list of 'SingleCellExperiment' objects |
| merge_seurat | Merge 'Seurat' objects |
| messager | Print messages |
| mofa_to_dro | Convert: 'MOFA' ==> 'DimReducObject' |
| output_dict | Output dictionary |
| process_seurat | Process a 'Seurat' object |
| read_data | Read data |
| save_data | Save data |
| sce_to_se | Convert: 'SingleCellExperiment' ==> 'SummarizedExperiment' |
| scKirby-package | scKirby: Automated ingestion and conversion of various... |
| scle_to_le | Convert: 'SingleCellLoomExperiment' ==> 'LoomExperiment' |
| set_graph | Set graphs |
| se_to_anndata | Convert: 'SummarizedExperiment' ==> 'AnnData' |
| set_obs | Set unstructured data |
| se_to_le | Convert: 'SummarizedExperiment' ==>... |
| se_to_list | Convert: 'SummarizedExperiment' ==> 'list' |
| se_to_loom | Convert: 'SummarizedExperiment' ==> 'loom' |
| se_to_sce | Convert: 'SummarizedExperiment' ==> 'SingleCellExperiment' |
| se_to_seurat | Convert: 'SummarizedExperiment' ==> 'Seurat' |
| set_uns | Set unstructured data |
| set_var | Set unstructured data |
| seurat1_to_list | Convert: 'Seurat (V1)' ==> 'list' |
| seurat_to_anndata | Convert: 'Seurat' ==> 'AnnData' |
| seurat_to_cds | Convert: 'Seurat' ==> 'CellDataSet' |
| seurat_to_h5seurat | Convert: 'Seurat' ==> 'H5Seurat' |
| seurat_to_le | Convert: 'Seurat' ==> 'LoomExperiment' |
| seurat_to_list | Convert: 'Seurat' ==> 'list' |
| seurat_to_se | Convert: 'Seurat' ==> 'SummarizedExperiment' |
| standardise_obs | Prepare metadata |
| stopper | Stop messages |
| to_anndata | To 'AnnData' |
| to_delayedarray | Convert: to 'DelayedArray' |
| to_graph | To graph |
| to_list | Convert: to 'list' |
| to_loom | Convert: to 'loom' |
| to_se | Convert: ==> 'SummarizedExperiment' |
| to_sparse | To 'sparseMatrix' |
| update_seurat | Update Seurat object |
