Expression Weighted Celltype Enrichment
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Documentation for package ‘EWCE’ version 1.12.0
Help Pages
| EWCE-package | EWCE: Expression Weighted Celltype Enrichment |
| add_res_to_merging_list | Add to results to merging list |
| bin_columns_into_quantiles | 'bin_columns_into_quantiles' |
| bin_specificity_into_quantiles | bin_specificity_into_quantiles |
| bootstrap_enrichment_test | Bootstrap cell type enrichment test |
| check_ewce_genelist_inputs | check_ewce_genelist_inputs |
| check_percent_hits | Get percentage of target cell type hits |
| controlled_geneset_enrichment | Celltype controlled geneset enrichment |
| ctd_to_sce | CellTypeDataset to SingleCellExperiment |
| drop_uninformative_genes | Drop uninformative genes |
| EWCE | EWCE: Expression Weighted Celltype Enrichment |
| ewce_expression_data | Bootstrap cell type enrichment test for transcriptome data |
| ewce_plot | Plot EWCE results |
| example_bootstrap_results | Example bootstrap enrichment results |
| example_transcriptome_results | Example bootstrap celltype enrichment test for transcriptome data |
| filter_ctd_genes | Filter genes in a CellTypeDataset |
| filter_genes_without_1to1_homolog | filter_genes_without_1to1_homolog |
| filter_nonorthologs | Filter non-orthologs |
| fix_bad_hgnc_symbols | fix_bad_hgnc_symbols |
| fix_bad_mgi_symbols | fix_bad_mgi_symbols - Given an expression matrix, wherein the rows are supposed to be MGI symbols, find those symbols which are not official MGI symbols, then check in the MGI synonm database for whether they match to a proper MGI symbol. Where a symbol is found to be an aliases for a gene that is already in the dataset, the combined reads are summed together. |
| fix_celltype_names | Fix celltype names |
| generate_bootstrap_plots | Generate bootstrap plots |
| generate_bootstrap_plots_for_transcriptome | Generate bootstrap plots |
| generate_celltype_data | Generate CellTypeData (CTD) file |
| get_celltype_table | get_celltype_table |
| is_delayed_array | Assess whether an object is a DelayedArray. |
| is_matrix | Assess whether an object is a Matrix |
| is_sparse_matrix | Assess whether an object is a sparse matrix |
| list_species | List all species |
| load_rdata | 'load_rdata' |
| merged_ewce | Multiple EWCE results from multiple studies |
| merge_ctd | Merge multiple CellTypeDataset references |
| merge_sce | Merge multiple 'SingleCellExperiment' objects |
| merge_two_expfiles | Merge two exp files |
| plot_ctd | Plot _CellTypeData_ metrics |
| prep.dendro | prep.dendro |
| sct_normalize | Normalize expression matrix |
| standardise_ctd | Convert a CellTypeDataset into standardized format |