Man pages for NathanSkene/EWCE
Expression Weighted Celltype Enrichment
| add_res_to_merging_list | Add to results to merging list |
| assign_cores | Assign cores |
| bin_columns_into_quantiles | 'bin_columns_into_quantiles' |
| bin_specificity_into_quantiles | bin_specificity_into_quantiles |
| bootstrap_enrichment_test | Bootstrap cell type enrichment test |
| bootstrap_plot | Bootstrap plot |
| bootstrap_plots_for_transcriptome | Bootstrap plot |
| calculate_meanexp_for_level | calculate_meanexp_for_level |
| calculate_specificity_for_level | Calculate specificity for one CTD level |
| cell_list_dist | cell_list_dist |
| check_annotLevels | check_annotLevels First, check the number of annotations... |
| check_args_for_bootstrap_plot_generation | check_args_for_bootstrap_plot_generation |
| check_bootstrap_args | check_bootstrap_args |
| check_controlled_args | check_controlled_args |
| check_ewce_expression_data_args | check_ewce_expression_data_args |
| check_ewce_genelist_inputs | check_ewce_genelist_inputs |
| check_full_results | check_full_results |
| check_generate_controlled_bootstrap_geneset | generate_controlled_bootstrap_geneset |
| check_group_name | Check group name |
| check_nas | Check NAs |
| check_numeric | Check numeric |
| check_percent_hits | Get percentage of target cell type hits |
| check_sce | Check SingleCellExperiment |
| check_species | Check species |
| compute_gene_counts | Compute gene counts |
| compute_gene_scores | Compute gene counts |
| controlled_geneset_enrichment | Celltype controlled geneset enrichment |
| convert_new_ewce_to_old | convert_new_ewce_to_old |
| convert_old_ewce_to_new | convert_old_ewce_to_new |
| create_background_multilist | Create background gene list for multiple species |
| create_list_network | 'create_list_network' |
| ctd_to_sce | CellTypeDataset to SingleCellExperiment |
| delayedarray_normalize | Efficiently normalize a DelayedArray |
| drop_nonexpressed_cells | Drop cells with zero gene counts |
| drop_nonexpressed_genes | Drop genes with zero counts |
| drop_uninformative_genes | Drop uninformative genes |
| dt_to_df | Convert a 'data.table' to a 'data.frame'. |
| ewce_expression_data | Bootstrap cell type enrichment test for transcriptome data |
| EWCE-package | EWCE: Expression Weighted Celltype Enrichment |
| ewce_plot | Plot EWCE results |
| example_bootstrap_results | Example bootstrap enrichment results |
| example_transcriptome_results | Example bootstrap celltype enrichment test for transcriptome... |
| extract_matrix | Extract a matrix from a CellTypeDataset |
| filter_ctd_genes | Filter genes in a CellTypeDataset |
| filter_genes_without_1to1_homolog | filter_genes_without_1to1_homolog |
| filter_nonorthologs | Filter non-orthologs |
| filter_variance_quantiles | Filter variance quantiles |
| fix_bad_hgnc_symbols | fix_bad_hgnc_symbols |
| fix_bad_mgi_symbols | fix_bad_mgi_symbols - Given an expression matrix, wherein the... |
| fix_celltype_names | Fix celltype names |
| fix_celltype_names_full_results | Fix celltype name in full results |
| generate_bootstrap_plots | Generate bootstrap plots |
| generate_bootstrap_plots_for_transcriptome | Generate bootstrap plots |
| generate_celltype_data | Generate CellTypeData (CTD) file |
| generate_controlled_bootstrap_geneset | generate_controlled_bootstrap_geneset |
| get_celltype_table | get_celltype_table |
| get_ctd_levels | Get the names of CellTypeDataset levels |
| get_ctd_matrix_names | Get CTD matrix names |
| get_exp_data_for_bootstrapped_genes | get_exp_data_for_bootstrapped_genes |
| get_sig_results | Extract significant results |
| get_summed_proportions | Get summed proportions |
| is_32bit | Checks whether OS is a 32-bit Windows |
| is_celltypedataset | Check whether object is a CellTypeDataset |
| is_ctd_standardised | Check whether a CellTypeDataset is standardised |
| 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' |
| max_ctd_depth | Get max CTD depth |
| merge_ctd | Merge multiple CellTypeDataset references |
| merged_ewce | Multiple EWCE results from multiple studies |
| merge_sce | Merge multiple 'SingleCellExperiment' objects |
| merge_sce_list | Merge of list of SingleCellExperiment objects |
| merge_two_expfiles | Merge two exp files |
| message_parallel | Print messages |
| messager | Print messages |
| myScalesComma | 'myScalesComma' |
| plot_ctd | Plot _CellTypeData_ metrics |
| plot_log_bootstrap_distributions | Plot log bootstrap distributions |
| plot_with_bootstrap_distributions | Plot with bootstrap distributions |
| prepare_genesize_control_network | Prepare genesize control network |
| prepare_tt | Prepare differential gene expression table |
| prep_dendro | Prepare dendrogram |
| prep.dendro | prep.dendro |
| report_dge | Report DGE |
| report_results | Report cell type enrichment results |
| run_deseq2 | Run DGE: 'DESeq2' |
| run_limma | Run DGE: 'limma' |
| run_mast | Run DGE: 'MAST' |
| sce_lists_apply | sce_lists_apply |
| sce_merged_apply | sce_merged_apply |
| sct_normalize | Normalize expression matrix |
| standardise_ctd | Convert a CellTypeDataset into standardized format |
| theme_graph | Get graph theme |
| to_dataframe | Convert object to data.frame |
| to_delayed_array | Convert object to DelayedArray |
| to_sparse_matrix | Convert object to sparse matrix |
